diff --git a/ChangeLog.md b/ChangeLog.md
index 68b62107b58e0..a3fe632c528d1 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -36,6 +36,9 @@ See docs/process.md for more on how version tagging works.
   the per-call garbage on such calls. The registration ABI gained size and
   triviality parameters, so object files built against an older `bind.h` need
   to be rebuilt. (#27610)
+- `emscripten_clear_timeout` now releases the runtime keepalive held by the
+  pending timeout, and both `emscripten_clear_timeout` and
+  `emscripten_clear_immediate` are no-ops for ids that already fired. (#27720)
 
 6.0.9 - 09/01/26
 ----------------
diff --git a/src/lib/libeventloop.js b/src/lib/libeventloop.js
index 042dcad37b652..2f4fc25a63d81 100644
--- a/src/lib/libeventloop.js
+++ b/src/lib/libeventloop.js
@@ -11,14 +11,32 @@ LibraryJSEventLoop = {
     throw 'unwind';
   },
 
+  // Just like setTimeout but returns an i32 that can be passed back to wasm
+  // rather than a JS object, and holds a runtime keepalive while pending.
   $safeSetTimeout__deps: ['$callUserCallback'],
   $safeSetTimeout__docs: '/** @param {number=} timeout */',
   $safeSetTimeout: (func, timeout) => {
     {{{ runtimeKeepalivePush() }}}
-    return setTimeout(() => {
+    // Slot 0 is reserved so that, like setTimeout, ids are always non-zero.
+    safeSetTimeout.mapping ||= [0];
+    var id = safeSetTimeout.mapping.length;
+    safeSetTimeout.mapping[id] = setTimeout(() => {
+      safeSetTimeout.mapping[id] = undefined;
       {{{ runtimeKeepalivePop() }}}
       callUserCallback(func);
     }, timeout);
+    return id;
+  },
+
+  // Clears a pending safeSetTimeout and releases its keepalive. No-op if the
+  // timeout has already fired or been cleared.
+  $safeClearTimeout__deps: ['$safeSetTimeout'],
+  $safeClearTimeout: (id) => {
+    var handle = safeSetTimeout.mapping?.[id];
+    if (!handle) return;
+    clearTimeout(handle);
+    safeSetTimeout.mapping[id] = undefined;
+    {{{ runtimeKeepalivePop() }}}
   },
 
   // Just like setImmediate but returns an i32 that can be passed back
@@ -43,13 +61,13 @@ LibraryJSEventLoop = {
   },
 
   // Just like clearImmediate but takes an i32 rather than an object.
+  // Returns true if the immediate was still pending.
   $clearImmediateWrapped: (id) => {
-#if ASSERTIONS
-    assert(id);
-    assert(setImmediateWrapped.mapping[id]);
-#endif
-    clearImmediate(setImmediateWrapped.mapping[id]);
+    var handle = setImmediateWrapped.mapping[id];
+    if (!handle) return false;
+    clearImmediate(handle);
     setImmediateWrapped.mapping[id] = undefined;
+    return true;
   },
 
   $emSetImmediate__deps: ['$setImmediateWrapped', '$clearImmediateWrapped', '$emClearImmediate'],
@@ -81,8 +99,10 @@ LibraryJSEventLoop = {
       }
       emClearImmediate = /**@type{function(number=)}*/((id) => {
         var index = id - __setImmediate_id_counter;
+        if (index < 0 || !__setImmediate_queue[index]) return false;
         // must preserve the order and count of elements in the queue, so replace the pending callback with an empty function
-        if (index >= 0 && index < __setImmediate_queue.length) __setImmediate_queue[index] = null;
+        __setImmediate_queue[index] = null;
+        return true;
       })
     }`,
   $emSetImmediate: undefined,
@@ -101,8 +121,9 @@ LibraryJSEventLoop = {
 
   emscripten_clear_immediate__deps: ['$emClearImmediate'],
   emscripten_clear_immediate: (id) => {
-    {{{ runtimeKeepalivePop(); }}}
-    emClearImmediate(id);
+    if (emClearImmediate(id)) {
+      {{{ runtimeKeepalivePop(); }}}
+    }
   },
 
   emscripten_set_immediate_loop__deps: ['$emSetImmediate', '$callUserCallback'],
@@ -124,13 +145,7 @@ LibraryJSEventLoop = {
   emscripten_set_timeout: (cb, msecs, userData) =>
     safeSetTimeout(() => {{{ makeDynCall('vp', 'cb') }}}(userData), msecs),
 
-#if AUDIO_WORKLET
-  // Use a wrapper function here since simply aliasing `clearTimeout` would
-  // cause the module to fail to load in the audio worklet context.
-  emscripten_clear_timeout: (id) => clearTimeout(id),
-#else
-  emscripten_clear_timeout: 'clearTimeout',
-#endif
+  emscripten_clear_timeout: '$safeClearTimeout',
 
   emscripten_set_timeout_loop__deps: ['$callUserCallback', 'emscripten_get_now'],
   emscripten_set_timeout_loop: (cb, msecs, userData) => {
diff --git a/src/lib/libsdl.js b/src/lib/libsdl.js
index a0e5e63f33e92..ccd5394ae16a9 100644
--- a/src/lib/libsdl.js
+++ b/src/lib/libsdl.js
@@ -2562,14 +2562,14 @@ var LibrarySDL = {
   },
 
   SDL_PauseAudio__proxy: 'sync',
-  SDL_PauseAudio__deps: ['$safeSetTimeout'],
+  SDL_PauseAudio__deps: ['$safeSetTimeout', '$safeClearTimeout'],
   SDL_PauseAudio: (pauseOn) => {
     if (!SDL.audio) {
       return;
     }
     if (pauseOn) {
       if (SDL.audio.timer !== undefined) {
-        clearTimeout(SDL.audio.timer);
+        safeClearTimeout(SDL.audio.timer);
         SDL.audio.numAudioTimersPending = 0;
         SDL.audio.timer = undefined;
       }
@@ -3579,8 +3579,9 @@ var LibrarySDL = {
       interval),
 
   SDL_RemoveTimer__proxy: 'sync',
+  SDL_RemoveTimer__deps: ['$safeClearTimeout'],
   SDL_RemoveTimer: (id) => {
-    clearTimeout(id);
+    safeClearTimeout(id);
     return true;
   },
 
diff --git a/test/codesize/test_codesize_hello_O0.json b/test/codesize/test_codesize_hello_O0.json
index 017298ab01b7c..0a131354a605f 100644
--- a/test/codesize/test_codesize_hello_O0.json
+++ b/test/codesize/test_codesize_hello_O0.json
@@ -1,10 +1,10 @@
 {
-  "a.out.js": 23579,
-  "a.out.js.gz": 8576,
+  "a.out.js": 23596,
+  "a.out.js.gz": 8582,
   "a.out.nodebug.wasm": 14279,
   "a.out.nodebug.wasm.gz": 7101,
-  "total": 37858,
-  "total_gz": 15677,
+  "total": 37875,
+  "total_gz": 15683,
   "sent": [
     "fd_write"
   ],
diff --git a/test/codesize/test_codesize_hello_dylink_all.json b/test/codesize/test_codesize_hello_dylink_all.json
index 19e642f329f77..2599da95e6573 100644
--- a/test/codesize/test_codesize_hello_dylink_all.json
+++ b/test/codesize/test_codesize_hello_dylink_all.json
@@ -1,7 +1,7 @@
 {
-  "a.out.js": 270520,
+  "a.out.js": 270695,
   "a.out.nodebug.wasm": 588289,
-  "total": 858809,
+  "total": 858984,
   "sent": [
     "IMG_Init",
     "IMG_Load",
diff --git a/test/codesize/test_codesize_minimal_O0.expected.js b/test/codesize/test_codesize_minimal_O0.expected.js
index a8d77958ced86..61b5952de1fd0 100644
--- a/test/codesize/test_codesize_minimal_O0.expected.js
+++ b/test/codesize/test_codesize_minimal_O0.expected.js
@@ -948,6 +948,7 @@ Module['FS_createPreloadedFile'] = FS.createPreloadedFile;
   'initRandomFill',
   'randomFill',
   'safeSetTimeout',
+  'safeClearTimeout',
   'setImmediateWrapped',
   'safeRequestAnimationFrame',
   'clearImmediateWrapped',
diff --git a/test/codesize/test_codesize_minimal_O0.json b/test/codesize/test_codesize_minimal_O0.json
index 00a34fec5ebd7..f960557acfdd1 100644
--- a/test/codesize/test_codesize_minimal_O0.json
+++ b/test/codesize/test_codesize_minimal_O0.json
@@ -1,10 +1,10 @@
 {
-  "a.out.js": 18784,
-  "a.out.js.gz": 6752,
+  "a.out.js": 18801,
+  "a.out.js.gz": 6758,
   "a.out.nodebug.wasm": 1071,
   "a.out.nodebug.wasm.gz": 636,
-  "total": 19855,
-  "total_gz": 7388,
+  "total": 19872,
+  "total_gz": 7394,
   "sent": [],
   "imports": [],
   "exports": [
diff --git a/test/codesize/test_unoptimized_code_size.json b/test/codesize/test_unoptimized_code_size.json
index 920e5a7844084..a6bc588a5bc49 100644
--- a/test/codesize/test_unoptimized_code_size.json
+++ b/test/codesize/test_unoptimized_code_size.json
@@ -1,16 +1,16 @@
 {
-  "hello_world.js": 54683,
-  "hello_world.js.gz": 17343,
+  "hello_world.js": 54705,
+  "hello_world.js.gz": 17355,
   "hello_world.wasm": 14279,
   "hello_world.wasm.gz": 7101,
   "no_asserts.js": 23596,
   "no_asserts.js.gz": 8277,
   "no_asserts.wasm": 11393,
   "no_asserts.wasm.gz": 5646,
-  "strict.js": 51834,
-  "strict.js.gz": 16342,
+  "strict.js": 51856,
+  "strict.js.gz": 16348,
   "strict.wasm": 14279,
   "strict.wasm.gz": 7098,
-  "total": 170064,
-  "total_gz": 61807
+  "total": 170108,
+  "total_gz": 61825
 }
diff --git a/test/test_emscripten_clear_timeout.c b/test/test_emscripten_clear_timeout.c
new file mode 100644
index 0000000000000..ea2073dcbf622
--- /dev/null
+++ b/test/test_emscripten_clear_timeout.c
@@ -0,0 +1,60 @@
+#include <assert.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <emscripten/eventloop.h>
+
+int fired_id;
+
+void never(void *arg) {
+  printf("cleared callback ran\n");
+  abort();
+}
+
+void fired(void *arg) {
+  printf("fired\n");
+  // Clearing an id that already fired must be a no-op.
+  emscripten_clear_timeout(fired_id);
+  emscripten_clear_timeout(fired_id);
+}
+
+void immediate_fired(void *arg) {
+  emscripten_clear_immediate(fired_id);
+  emscripten_clear_immediate(fired_id);
+}
+
+// Only runs if the runtime actually exits.
+void at_exit() {
+  printf("done\n");
+}
+
+int main() {
+  atexit(at_exit);
+#if MODE_CLEARED
+  // Clearing a pending timeout releases its keepalive so the runtime exits
+  // from main without waiting for it (a leak fails the check below; a timer
+  // that was not actually cleared aborts when it fires).
+  int id = emscripten_set_timeout(never, 1000, NULL);
+  assert(emscripten_runtime_keepalive_check());
+  emscripten_clear_timeout(id);
+  assert(!emscripten_runtime_keepalive_check());
+  return 42;
+#elif MODE_IDEMPOTENT
+  int id = emscripten_set_timeout(never, 1000, NULL);
+  emscripten_clear_timeout(id);
+  emscripten_clear_timeout(id);
+  fired_id = emscripten_set_timeout(fired, 0, NULL);
+  // Still-pending timer must keep the runtime alive until it fires.
+  emscripten_set_timeout(fired, 50, NULL);
+  return 0;
+#elif MODE_IMMEDIATE
+  int id = emscripten_set_immediate(never, NULL);
+  emscripten_clear_immediate(id);
+  emscripten_clear_immediate(id);
+  fired_id = emscripten_set_immediate(immediate_fired, NULL);
+  emscripten_set_timeout(fired, 50, NULL);
+  return 0;
+#else
+  emscripten_set_timeout(fired, 50, NULL);
+  return 0;
+#endif
+}
diff --git a/test/test_other.py b/test/test_other.py
index d2c96fa81755b..bd63374a7c13b 100644
--- a/test/test_other.py
+++ b/test/test_other.py
@@ -13724,6 +13724,15 @@ def test_emscripten_set_timeout(self):
   def test_emscripten_set_timeout_loop(self):
     self.do_runf('emscripten_set_timeout_loop.c', args=['-pthread', '-sPROXY_TO_PTHREAD'])
 
+  @parameterized({
+    'fires': ([], 0, 'fired\ndone\n'),
+    'cleared': (['-DMODE_CLEARED'], 42, 'done\n'),
+    'idempotent': (['-DMODE_IDEMPOTENT'], 0, 'fired\nfired\ndone\n'),
+    'immediate': (['-DMODE_IMMEDIATE'], 0, 'fired\ndone\n'),
+  })
+  def test_emscripten_clear_timeout(self, cflags, returncode, expected):
+    self.do_runf('test_emscripten_clear_timeout.c', expected, cflags=['-sEXIT_RUNTIME'] + cflags, assert_returncode=returncode)
+
   @parameterized({
     '': ([],),
     'asyncify': (['-sASYNCIFY'],),