diff --git a/.changeset/stdio-skip-non-json.md b/.changeset/stdio-skip-non-json.md
new file mode 100644
index 000000000..d20b740c9
--- /dev/null
+++ b/.changeset/stdio-skip-non-json.md
@@ -0,0 +1,5 @@
+---
+'@modelcontextprotocol/core': patch
+---
+
+`ReadBuffer.readMessage()` now silently skips non-JSON lines instead of throwing `SyntaxError`. This prevents noisy `onerror` callbacks when hot-reload tools (tsx, nodemon) write debug output like "Gracefully restarting..." to stdout. Lines that parse as JSON but fail JSONRPC schema validation still throw.
diff --git a/packages/core/src/shared/stdio.ts b/packages/core/src/shared/stdio.ts
index 773860770..7283a5ef9 100644
--- a/packages/core/src/shared/stdio.ts
+++ b/packages/core/src/shared/stdio.ts
@@ -12,18 +12,28 @@ export class ReadBuffer {
     }
 
     readMessage(): JSONRPCMessage | null {
-        if (!this._buffer) {
-            return null;
+        while (this._buffer) {
+            const index = this._buffer.indexOf('\n');
+            if (index === -1) {
+                return null;
+            }
+
+            const line = this._buffer.toString('utf8', 0, index).replace(/\r$/, '');
+            this._buffer = this._buffer.subarray(index + 1);
+
+            try {
+                return deserializeMessage(line);
+            } catch (error) {
+                // Skip non-JSON lines (e.g., debug output from hot-reload tools like
+                // tsx or nodemon that write to stdout). Schema validation errors still
+                // throw so malformed-but-valid-JSON messages surface via onerror.
+                if (error instanceof SyntaxError) {
+                    continue;
+                }
+                throw error;
+            }
         }
-
-        const index = this._buffer.indexOf('\n');
-        if (index === -1) {
-            return null;
-        }
-
-        const line = this._buffer.toString('utf8', 0, index).replace(/\r$/, '');
-        this._buffer = this._buffer.subarray(index + 1);
-        return deserializeMessage(line);
+        return null;
     }
 
     clear(): void {
diff --git a/packages/core/test/shared/stdio.test.ts b/packages/core/test/shared/stdio.test.ts
index 7e880aa57..65d1de0ea 100644
--- a/packages/core/test/shared/stdio.test.ts
+++ b/packages/core/test/shared/stdio.test.ts
@@ -33,3 +33,83 @@ test('should be reusable after clearing', () => {
     readBuffer.append(Buffer.from('\n'));
     expect(readBuffer.readMessage()).toEqual(testMessage);
 });
+
+describe('non-JSON line filtering', () => {
+    test('should skip empty lines', () => {
+        const readBuffer = new ReadBuffer();
+        readBuffer.append(Buffer.from('\n\n' + JSON.stringify(testMessage) + '\n\n'));
+
+        expect(readBuffer.readMessage()).toEqual(testMessage);
+        expect(readBuffer.readMessage()).toBeNull();
+    });
+
+    test('should skip non-JSON lines before a valid message', () => {
+        const readBuffer = new ReadBuffer();
+        readBuffer.append(Buffer.from('Debug: Starting server\n' + 'Warning: Something happened\n' + JSON.stringify(testMessage) + '\n'));
+
+        expect(readBuffer.readMessage()).toEqual(testMessage);
+        expect(readBuffer.readMessage()).toBeNull();
+    });
+
+    test('should skip non-JSON lines interleaved with multiple valid messages', () => {
+        const readBuffer = new ReadBuffer();
+        const message1: JSONRPCMessage = { jsonrpc: '2.0', method: 'method1' };
+        const message2: JSONRPCMessage = { jsonrpc: '2.0', method: 'method2' };
+
+        readBuffer.append(
+            Buffer.from(
+                'Debug line 1\n' +
+                    JSON.stringify(message1) +
+                    '\n' +
+                    'Debug line 2\n' +
+                    'Another non-JSON line\n' +
+                    JSON.stringify(message2) +
+                    '\n'
+            )
+        );
+
+        expect(readBuffer.readMessage()).toEqual(message1);
+        expect(readBuffer.readMessage()).toEqual(message2);
+        expect(readBuffer.readMessage()).toBeNull();
+    });
+
+    test('should preserve incomplete JSON at end of buffer until completed', () => {
+        const readBuffer = new ReadBuffer();
+        readBuffer.append(Buffer.from('{"jsonrpc": "2.0", "method": "test"'));
+        expect(readBuffer.readMessage()).toBeNull();
+
+        readBuffer.append(Buffer.from('}\n'));
+        expect(readBuffer.readMessage()).toEqual({ jsonrpc: '2.0', method: 'test' });
+    });
+
+    test('should skip lines with unbalanced braces', () => {
+        const readBuffer = new ReadBuffer();
+        readBuffer.append(Buffer.from('{incomplete\n' + 'incomplete}\n' + JSON.stringify(testMessage) + '\n'));
+
+        expect(readBuffer.readMessage()).toEqual(testMessage);
+        expect(readBuffer.readMessage()).toBeNull();
+    });
+
+    test('should skip lines that look like JSON but fail to parse', () => {
+        const readBuffer = new ReadBuffer();
+        readBuffer.append(Buffer.from('{invalidJson: true}\n' + JSON.stringify(testMessage) + '\n'));
+
+        expect(readBuffer.readMessage()).toEqual(testMessage);
+        expect(readBuffer.readMessage()).toBeNull();
+    });
+
+    test('should tolerate leading/trailing whitespace around valid JSON', () => {
+        const readBuffer = new ReadBuffer();
+        const message: JSONRPCMessage = { jsonrpc: '2.0', method: 'test' };
+        readBuffer.append(Buffer.from('  ' + JSON.stringify(message) + '  \n'));
+
+        expect(readBuffer.readMessage()).toEqual(message);
+    });
+
+    test('should still throw on valid JSON that fails schema validation', () => {
+        const readBuffer = new ReadBuffer();
+        readBuffer.append(Buffer.from('{"not": "a jsonrpc message"}\n'));
+
+        expect(() => readBuffer.readMessage()).toThrow();
+    });
+});