diff --git a/javascript/extractor/src/com/semmle/js/extractor/AutoBuild.java b/javascript/extractor/src/com/semmle/js/extractor/AutoBuild.java
index 416fa237e97e..82dcc0bc2a7d 100644
--- a/javascript/extractor/src/com/semmle/js/extractor/AutoBuild.java
+++ b/javascript/extractor/src/com/semmle/js/extractor/AutoBuild.java
@@ -794,7 +794,7 @@ private CompletableFuture<?> extractSource() throws IOException {
       }
     }
     // exclude files in output directories as configured in tsconfig.json
-    filesToExtract.removeIf(f -> outDirs.stream().anyMatch(od -> f.startsWith(od)));
+    filesToExtract.removeIf(f -> FileType.forFileExtension(f.toFile()) == FileType.JS && outDirs.stream().anyMatch(od -> f.startsWith(od)));
 
     DependencyInstallationResult dependencyInstallationResult = DependencyInstallationResult.empty;
     if (!tsconfigFiles.isEmpty()) {
diff --git a/javascript/ql/src/change-notes/2026-01-08-out-dir-filtering.md b/javascript/ql/src/change-notes/2026-01-08-out-dir-filtering.md
new file mode 100644
index 000000000000..0fa9d6f05c76
--- /dev/null
+++ b/javascript/ql/src/change-notes/2026-01-08-out-dir-filtering.md
@@ -0,0 +1,6 @@
+---
+category: fix
+---
+* Fixed a bug that would cause `.ts` files to be skipped when they were inside the `outDir` of
+  the corresponding `tsconfig.json` file. Now only JavaScript files are excluded when they appear
+  in the `outDir`.