diff --git a/doc/api/deprecations.md b/doc/api/deprecations.md
index 1e7ff6f682347b..fb830914ceb99a 100644
--- a/doc/api/deprecations.md
+++ b/doc/api/deprecations.md
@@ -3313,6 +3313,9 @@ Values other than `undefined`, `null`, integer numbers, and integer strings
 
 <!-- YAML
 changes:
+  - version: REPLACEME
+    pr-url: https://github.com/nodejs/node/pull/51179
+    description: Runtime deprecation.
   - version:
     - v18.8.0
     - v16.18.0
@@ -3320,9 +3323,11 @@ changes:
     description: Documentation-only deprecation.
 -->
 
-Type: Documentation-only
+Type: Runtime
 
-The [`--trace-atomics-wait`][] flag is deprecated.
+The [`--trace-atomics-wait`][] flag is deprecated because
+it uses the V8 hook `SetAtomicsWaitCallback`,
+that will be removed in a future V8 release.
 
 ### DEP0166: Double slashes in imports and exports targets
 
diff --git a/src/node.cc b/src/node.cc
index deaed9ec3d74a9..cec88c4f4ecd84 100644
--- a/src/node.cc
+++ b/src/node.cc
@@ -258,6 +258,10 @@ void Environment::InitializeDiagnostics() {
   if (options_->trace_uncaught)
     isolate_->SetCaptureStackTraceForUncaughtExceptions(true);
   if (options_->trace_atomics_wait) {
+    ProcessEmitDeprecationWarning(
+        Environment::GetCurrent(isolate_),
+        "The flag --trace-atomics-wait is deprecated.",
+        "DEP0165");
     isolate_->SetAtomicsWaitCallback(AtomicsWaitCallback, this);
     AddCleanupHook([](void* data) {
       Environment* env = static_cast<Environment*>(data);
diff --git a/test/parallel/test-trace-atomic-deprecation.js b/test/parallel/test-trace-atomic-deprecation.js
new file mode 100644
index 00000000000000..10434c417518fd
--- /dev/null
+++ b/test/parallel/test-trace-atomic-deprecation.js
@@ -0,0 +1,14 @@
+'use strict';
+
+const common = require('../common');
+const assert = require('assert');
+const { test } = require('node:test');
+
+test('should emit deprecation warning DEP0165', async () => {
+  await common.spawnPromisified(process.execPath, ['--trace-atomics-wait', '-e', '{}'])
+        .then(common.mustCall(({ code, stdout, stderr }) => {
+          assert.strictEqual(code, 0);
+          assert.strictEqual(stdout, '');
+          assert.match(stderr, /\[DEP0165\] DeprecationWarning:/);
+        }));
+});