diff --git a/src/ir/intrinsics.cpp b/src/ir/intrinsics.cpp
index b2a5e1ff11a..6dd4c072324 100644
--- a/src/ir/intrinsics.cpp
+++ b/src/ir/intrinsics.cpp
@@ -101,29 +101,29 @@ std::vector<Name> Intrinsics::getConfigureAllFunctions(Call* call) {
   return ret;
 }
 
-std::vector<Name> Intrinsics::getConfigureAllFunctions() {
-  // ConfigureAll in a start function makes its functions callable.
+std::vector<Name> Intrinsics::getJSCalledFunctions() {
+  std::vector<Name> ret;
+  for (auto& func : module.functions) {
+    if (getAnnotations(func.get()).jsCalled) {
+      ret.push_back(func->name);
+    }
+  }
+
+  // ConfigureAlls in a start function make their functions callable.
   if (module.start) {
     auto* start = module.getFunction(module.start);
     if (!start->imported()) {
       FindAll<Call> calls(start->body);
-      // Look for the (single) configureAll.
-      Call* configureAll = nullptr;
       for (auto* call : calls.list) {
         if (isConfigureAll(call)) {
-          if (configureAll) {
-            Fatal() << "Multiple configureAlls";
-          } else {
-            configureAll = call;
+          for (auto name : getConfigureAllFunctions(call)) {
+            ret.push_back(name);
           }
         }
       }
-      if (configureAll) {
-        return getConfigureAllFunctions(configureAll);
-      }
     }
   }
-  return {};
+  return ret;
 }
 
 } // namespace wasm
diff --git a/src/ir/intrinsics.h b/src/ir/intrinsics.h
index 51ac3a6436b..9be2caebc7d 100644
--- a/src/ir/intrinsics.h
+++ b/src/ir/intrinsics.h
@@ -109,8 +109,11 @@ class Intrinsics {
   //
   // where the segment $seg is of size N.
   std::vector<Name> getConfigureAllFunctions(Call* call);
-  // As above, but looks through the module to find the configureAll.
-  std::vector<Name> getConfigureAllFunctions();
+
+  // Returns the names of all functions that are JS-called. That includes ones
+  // in configureAll (which we look through the module for), and also those
+  // annotated with @binaryen.js.called.
+  std::vector<Name> getJSCalledFunctions();
 
   // Get the code annotations for an expression in a function.
   CodeAnnotation getAnnotations(Expression* curr, Function* func) {
@@ -149,6 +152,9 @@ class Intrinsics {
       if (!ret.removableIfUnused) {
         ret.removableIfUnused = funcAnnotations.removableIfUnused;
       }
+      if (!ret.jsCalled) {
+        ret.jsCalled = funcAnnotations.jsCalled;
+      }
     }
 
     return ret;
diff --git a/src/ir/possible-contents.cpp b/src/ir/possible-contents.cpp
index c018cf628d7..06825343d1f 100644
--- a/src/ir/possible-contents.cpp
+++ b/src/ir/possible-contents.cpp
@@ -2454,8 +2454,8 @@ Flower::Flower(Module& wasm, const PassOptions& options)
     }
   }
 
-  // configureAll functions are called from outside the module, as if exported.
-  for (auto func : Intrinsics(wasm).getConfigureAllFunctions()) {
+  // JS-called functions are called from outside the module, as if exported.
+  for (auto func : Intrinsics(wasm).getJSCalledFunctions()) {
     calledFromOutside.insert(func);
   }
 
diff --git a/src/parser/contexts.h b/src/parser/contexts.h
index 3978afff45d..5ab172224e9 100644
--- a/src/parser/contexts.h
+++ b/src/parser/contexts.h
@@ -1317,6 +1317,8 @@ struct AnnotationParserCtx {
         inlineHint = &a;
       } else if (a.kind == Annotations::RemovableIfUnusedHint) {
         ret.removableIfUnused = true;
+      } else if (a.kind == Annotations::JSCalledHint) {
+        ret.jsCalled = true;
       }
     }
 
diff --git a/src/passes/GlobalTypeOptimization.cpp b/src/passes/GlobalTypeOptimization.cpp
index 5ea29f8e335..5ecc9ebae0a 100644
--- a/src/passes/GlobalTypeOptimization.cpp
+++ b/src/passes/GlobalTypeOptimization.cpp
@@ -420,7 +420,7 @@ struct GlobalTypeOptimization : public Pass {
     if (!wasm.features.hasCustomDescriptors()) {
       return;
     }
-    for (auto func : Intrinsics(wasm).getConfigureAllFunctions()) {
+    for (auto func : Intrinsics(wasm).getJSCalledFunctions()) {
       // Look at the result types being returned to JS and make sure we preserve
       // any configured prototypes they might expose.
       for (auto type : wasm.getFunction(func)->getResults()) {
diff --git a/src/passes/Print.cpp b/src/passes/Print.cpp
index d92a412dbbd..35b5a3076ec 100644
--- a/src/passes/Print.cpp
+++ b/src/passes/Print.cpp
@@ -2797,6 +2797,12 @@ void PrintSExpression::printCodeAnnotations(Expression* curr) {
       restoreNormalColor(o);
       doIndent(o, indent);
     }
+    if (annotation.jsCalled) {
+      Colors::grey(o);
+      o << "(@" << Annotations::JSCalledHint << ")\n";
+      restoreNormalColor(o);
+      doIndent(o, indent);
+    }
   }
 }
 
diff --git a/src/passes/RemoveUnusedModuleElements.cpp b/src/passes/RemoveUnusedModuleElements.cpp
index 64f56744624..c52f9872246 100644
--- a/src/passes/RemoveUnusedModuleElements.cpp
+++ b/src/passes/RemoveUnusedModuleElements.cpp
@@ -184,7 +184,16 @@ struct Noter : public PostWalker<Noter, UnifiedExpressionVisitor<Noter>> {
     noteCallRef(curr->target->type.getHeapType());
   }
 
-  void visitRefFunc(RefFunc* curr) { noteRefFunc(curr->func); }
+  void visitRefFunc(RefFunc* curr) {
+    // If the target is js-called then a reference is as strong as a use.
+    auto target = curr->func;
+    Intrinsics intrinsics(*getModule());
+    if (intrinsics.getAnnotations(getModule()->getFunction(target)).jsCalled) {
+      use({ModuleElementKind::Function, target});
+    } else {
+      noteRefFunc(target);
+    }
+  }
 
   void visitStructGet(StructGet* curr) {
     if (curr->ref->type == Type::unreachable || curr->ref->type.isNull()) {
diff --git a/src/passes/SignaturePruning.cpp b/src/passes/SignaturePruning.cpp
index d1f1a14456d..cb5155a7a14 100644
--- a/src/passes/SignaturePruning.cpp
+++ b/src/passes/SignaturePruning.cpp
@@ -176,9 +176,10 @@ struct SignaturePruning : public Pass {
       allInfo[tag->type].optimizable = false;
     }
 
-    // configureAll functions are signature-called, and must also not be
-    // modified.
-    for (auto func : Intrinsics(*module).getConfigureAllFunctions()) {
+    // Signature-called functions must also not be modified.
+    // TODO: Explore whether removing parameters from the end could be
+    //       beneficial (check if it does not regress call performance with JS).
+    for (auto func : Intrinsics(*module).getJSCalledFunctions()) {
       allInfo[module->getFunction(func)->type.getHeapType()].optimizable =
         false;
     }
diff --git a/src/passes/SignatureRefining.cpp b/src/passes/SignatureRefining.cpp
index b86a4a9eb60..67132733ec1 100644
--- a/src/passes/SignatureRefining.cpp
+++ b/src/passes/SignatureRefining.cpp
@@ -162,9 +162,8 @@ struct SignatureRefining : public Pass {
       }
     }
 
-    // configureAll functions are signature-called, which means their params
-    // must not be refined.
-    for (auto func : Intrinsics(*module).getConfigureAllFunctions()) {
+    // Signature-called functions must not have params refined.
+    for (auto func : Intrinsics(*module).getJSCalledFunctions()) {
       allInfo[module->getFunction(func)->type.getHeapType()].canModifyParams =
         false;
     }
diff --git a/src/passes/StripToolchainAnnotations.cpp b/src/passes/StripToolchainAnnotations.cpp
index 6118998eabf..c590afe964d 100644
--- a/src/passes/StripToolchainAnnotations.cpp
+++ b/src/passes/StripToolchainAnnotations.cpp
@@ -43,6 +43,7 @@ struct StripToolchainAnnotations
       // Remove the toolchain-specific annotations.
       auto& annotation = iter->second;
       annotation.removableIfUnused = false;
+      annotation.jsCalled = false;
 
       // If nothing remains, remove the entire annotation.
       if (annotation == CodeAnnotation()) {
diff --git a/src/passes/Unsubtyping.cpp b/src/passes/Unsubtyping.cpp
index 08e1c47feda..629d86c34c7 100644
--- a/src/passes/Unsubtyping.cpp
+++ b/src/passes/Unsubtyping.cpp
@@ -612,7 +612,7 @@ struct Unsubtyping : Pass, Noter<Unsubtyping> {
       return;
     }
     Type anyref(HeapType::any, Nullable);
-    for (auto func : Intrinsics(wasm).getConfigureAllFunctions()) {
+    for (auto func : Intrinsics(wasm).getJSCalledFunctions()) {
       // Parameter types flow into Wasm and are implicitly cast from any.
       for (auto type : wasm.getFunction(func)->getParams()) {
         if (Type::isSubType(type, anyref)) {
diff --git a/src/wasm-annotations.h b/src/wasm-annotations.h
index fec7f067795..17911a78ecb 100644
--- a/src/wasm-annotations.h
+++ b/src/wasm-annotations.h
@@ -28,6 +28,7 @@ namespace wasm::Annotations {
 extern const Name BranchHint;
 extern const Name InlineHint;
 extern const Name RemovableIfUnusedHint;
+extern const Name JSCalledHint;
 
 } // namespace wasm::Annotations
 
diff --git a/src/wasm-binary.h b/src/wasm-binary.h
index 3bd3199b67a..125040aa2d2 100644
--- a/src/wasm-binary.h
+++ b/src/wasm-binary.h
@@ -1442,6 +1442,7 @@ class WasmBinaryWriter {
   std::optional<BufferWithRandomAccess> getBranchHintsBuffer();
   std::optional<BufferWithRandomAccess> getInlineHintsBuffer();
   std::optional<BufferWithRandomAccess> getRemovableIfUnusedHintsBuffer();
+  std::optional<BufferWithRandomAccess> getJSCalledHintsBuffer();
 
   // helpers
   void writeInlineString(std::string_view name);
@@ -1734,7 +1735,8 @@ class WasmBinaryReader {
 
   void readBranchHints(size_t payloadLen);
   void readInlineHints(size_t payloadLen);
-  void readremovableIfUnusedHints(size_t payloadLen);
+  void readRemovableIfUnusedHints(size_t payloadLen);
+  void readJSCalledHints(size_t payloadLen);
 
   std::tuple<Address, Address, Index, MemoryOrder>
   readMemoryAccess(bool isAtomic, bool isRMW);
diff --git a/src/wasm.h b/src/wasm.h
index e74d6532ac2..87258b14c36 100644
--- a/src/wasm.h
+++ b/src/wasm.h
@@ -2245,15 +2245,23 @@ struct CodeAnnotation {
   static const uint8_t AlwaysInline = 127;
   std::optional<uint8_t> inline_;
 
-  // Toolchain hint: If this expression's result is unused, then the entire
-  // thing can be considered dead and removable. See
-  //
+  // Toolchain hints, see
   // https://github.com/WebAssembly/binaryen/wiki/Optimizer-Cookbook#intrinsics
+
+  // If this expression's result is unused, then the entire thing can be
+  // considered dead and removable.
   bool removableIfUnused = false;
 
+  // This should be assumed to be called from JS, even in closed world. Being
+  // called from JS means that the call happens in a non-typed way, with only
+  // the signature mattering ("signature-called"). In particular, rec group type
+  // identity does not matter for such functions.
+  bool jsCalled = false;
+
   bool operator==(const CodeAnnotation& other) const {
     return branchLikely == other.branchLikely && inline_ == other.inline_ &&
-           removableIfUnused == other.removableIfUnused;
+           removableIfUnused == other.removableIfUnused &&
+           jsCalled == other.jsCalled;
   }
 };
 
diff --git a/src/wasm/wasm-binary.cpp b/src/wasm/wasm-binary.cpp
index 85768b55fbc..23077d236a9 100644
--- a/src/wasm/wasm-binary.cpp
+++ b/src/wasm/wasm-binary.cpp
@@ -1628,6 +1628,7 @@ std::optional<BufferWithRandomAccess> WasmBinaryWriter::writeCodeAnnotations() {
   append(getBranchHintsBuffer());
   append(getInlineHintsBuffer());
   append(getRemovableIfUnusedHintsBuffer());
+  append(getJSCalledHintsBuffer());
   return ret;
 }
 
@@ -1783,6 +1784,17 @@ WasmBinaryWriter::getRemovableIfUnusedHintsBuffer() {
     });
 }
 
+std::optional<BufferWithRandomAccess>
+WasmBinaryWriter::getJSCalledHintsBuffer() {
+  return writeExpressionHints(
+    Annotations::JSCalledHint,
+    [](const CodeAnnotation& annotation) { return annotation.jsCalled; },
+    [](const CodeAnnotation& annotation, BufferWithRandomAccess& buffer) {
+      // Hint size, always empty.
+      buffer << U32LEB(0);
+    });
+}
+
 void WasmBinaryWriter::writeData(const char* data, size_t size) {
   for (size_t i = 0; i < size; i++) {
     o << int8_t(data[i]);
@@ -2055,7 +2067,8 @@ void WasmBinaryReader::preScan() {
 
       if (sectionName == Annotations::BranchHint ||
           sectionName == Annotations::InlineHint ||
-          sectionName == Annotations::RemovableIfUnusedHint) {
+          sectionName == Annotations::RemovableIfUnusedHint ||
+          sectionName == Annotations::JSCalledHint) {
         // Code annotations require code locations.
         // TODO: We could note which functions require code locations, as an
         //       optimization.
@@ -2215,8 +2228,11 @@ void WasmBinaryReader::readCustomSection(size_t payloadLen) {
   } else if (sectionName == Annotations::RemovableIfUnusedHint) {
     deferredAnnotationSections.push_back(
       AnnotationSectionInfo{pos, [this, payloadLen]() {
-                              this->readremovableIfUnusedHints(payloadLen);
+                              this->readRemovableIfUnusedHints(payloadLen);
                             }});
+  } else if (sectionName == Annotations::JSCalledHint) {
+    deferredAnnotationSections.push_back(AnnotationSectionInfo{
+      pos, [this, payloadLen]() { this->readJSCalledHints(payloadLen); }});
   } else {
     // an unfamiliar custom section
     if (sectionName.equals(BinaryConsts::CustomSections::Linking)) {
@@ -5527,7 +5543,7 @@ void WasmBinaryReader::readInlineHints(size_t payloadLen) {
     });
 }
 
-void WasmBinaryReader::readremovableIfUnusedHints(size_t payloadLen) {
+void WasmBinaryReader::readRemovableIfUnusedHints(size_t payloadLen) {
   readExpressionHints(Annotations::RemovableIfUnusedHint,
                       payloadLen,
                       [&](CodeAnnotation& annotation) {
@@ -5540,6 +5556,18 @@ void WasmBinaryReader::readremovableIfUnusedHints(size_t payloadLen) {
                       });
 }
 
+void WasmBinaryReader::readJSCalledHints(size_t payloadLen) {
+  readExpressionHints(
+    Annotations::JSCalledHint, payloadLen, [&](CodeAnnotation& annotation) {
+      auto size = getU32LEB();
+      if (size != 0) {
+        throwError("bad jsCalledHint size");
+      }
+
+      annotation.jsCalled = true;
+    });
+}
+
 std::tuple<Address, Address, Index, MemoryOrder>
 WasmBinaryReader::readMemoryAccess(bool isAtomic, bool isRMW) {
   auto rawAlignment = getU32LEB();
diff --git a/src/wasm/wasm-ir-builder.cpp b/src/wasm/wasm-ir-builder.cpp
index fd656f9b0fb..23ff8764971 100644
--- a/src/wasm/wasm-ir-builder.cpp
+++ b/src/wasm/wasm-ir-builder.cpp
@@ -2664,16 +2664,19 @@ void IRBuilder::applyAnnotations(Expression* expr,
   }
 
   if (annotation.inline_) {
-    // Only possible inside functions.
     assert(func);
     func->codeAnnotations[expr].inline_ = annotation.inline_;
   }
 
   if (annotation.removableIfUnused) {
-    // Only possible inside functions.
     assert(func);
     func->codeAnnotations[expr].removableIfUnused = true;
   }
+
+  if (annotation.jsCalled) {
+    assert(func);
+    func->codeAnnotations[expr].jsCalled = true;
+  }
 }
 
 } // namespace wasm
diff --git a/src/wasm/wasm.cpp b/src/wasm/wasm.cpp
index 4e901c152de..959b6cd4bfe 100644
--- a/src/wasm/wasm.cpp
+++ b/src/wasm/wasm.cpp
@@ -70,6 +70,7 @@ namespace Annotations {
 const Name BranchHint = "metadata.code.branch_hint";
 const Name InlineHint = "metadata.code.inline";
 const Name RemovableIfUnusedHint = "binaryen.removable.if.unused";
+const Name JSCalledHint = "binaryen.js.called";
 
 } // namespace Annotations
 
diff --git a/test/lit/js-called.wast b/test/lit/js-called.wast
new file mode 100644
index 00000000000..5766fb94550
--- /dev/null
+++ b/test/lit/js-called.wast
@@ -0,0 +1,24 @@
+;; NOTE: Assertions have been generated by update_lit_checks.py --all-items and should not be edited.
+
+;; RUN: wasm-opt -all             %s -S -o - | filecheck %s
+;; RUN: wasm-opt -all --roundtrip %s -S -o - | filecheck %s
+
+;; Test text and binary handling of @binaryen.js.called.
+
+(module
+  ;; CHECK:      (type $0 (func))
+
+  ;; CHECK:      (@binaryen.js.called)
+  ;; CHECK-NEXT: (func $func-annotation (type $0)
+  ;; CHECK-NEXT:  (drop
+  ;; CHECK-NEXT:   (i32.const 0)
+  ;; CHECK-NEXT:  )
+  ;; CHECK-NEXT: )
+  (@binaryen.js.called)
+  (func $func-annotation
+    (drop
+      (i32.const 0)
+    )
+  )
+)
+
diff --git a/test/lit/passes/remove-unused-module-elements-js-called.wast b/test/lit/passes/remove-unused-module-elements-js-called.wast
new file mode 100644
index 00000000000..f26223051e5
--- /dev/null
+++ b/test/lit/passes/remove-unused-module-elements-js-called.wast
@@ -0,0 +1,39 @@
+;; NOTE: Assertions have been generated by update_lit_checks.py --all-items and should not be edited.
+
+;; RUN: foreach %s %t wasm-opt --remove-unused-module-elements --closed-world -all -S -o - | filecheck %s
+
+(module
+  ;; CHECK:      (type $0 (func))
+
+  ;; CHECK:      (elem declare func $js.called.referred)
+
+  ;; CHECK:      (export "export" (func $export))
+
+  ;; CHECK:      (@binaryen.js.called)
+  ;; CHECK-NEXT: (func $js.called.referred (type $0)
+  ;; CHECK-NEXT:  (drop
+  ;; CHECK-NEXT:   (i32.const 10)
+  ;; CHECK-NEXT:  )
+  ;; CHECK-NEXT: )
+  (@binaryen.js.called)
+  (func $js.called.referred
+    ;; This is jsCalled, and referred below, so it is kept.
+    (drop (i32.const 10))
+  )
+
+  ;; CHECK:      (func $export (type $0)
+  ;; CHECK-NEXT:  (drop
+  ;; CHECK-NEXT:   (ref.func $js.called.referred)
+  ;; CHECK-NEXT:  )
+  ;; CHECK-NEXT: )
+  (func $export (export "export")
+    (drop (ref.func $js.called.referred))
+  )
+
+  (@binaryen.js.called)
+  (func $js.called.unreferred
+    ;; This is jsCalled, and not referred anywhere. The annotation does not
+    ;; stop the function from being removed entirely.
+    (drop (i32.const 20))
+  )
+)
diff --git a/test/lit/passes/strip-toolchain-annotations-func.wast b/test/lit/passes/strip-toolchain-annotations-func.wast
index 564676179ed..80cf695273c 100644
--- a/test/lit/passes/strip-toolchain-annotations-func.wast
+++ b/test/lit/passes/strip-toolchain-annotations-func.wast
@@ -31,8 +31,9 @@
   ;; CHECK-NEXT: )
   (@binaryen.removable.if.unused)
   (@metadata.code.inline "\00")
+  (@binaryen.js.called)
   (func $test-func-d
-    ;; Reverse order of above.
+    ;; Reverse order of above, and also includes js.called which is removed.
   )
 )