diff --git a/javascript/ql/lib/semmle/javascript/security/dataflow/MissingRateLimiting.qll b/javascript/ql/lib/semmle/javascript/security/dataflow/MissingRateLimiting.qll
index 5f4ad1b3d73e..8dd9c4831446 100644
--- a/javascript/ql/lib/semmle/javascript/security/dataflow/MissingRateLimiting.qll
+++ b/javascript/ql/lib/semmle/javascript/security/dataflow/MissingRateLimiting.qll
@@ -191,3 +191,21 @@ class RouteHandlerLimitedByRateLimiterFlexible extends RateLimitingMiddleware in
 private class FastifyRateLimiter extends RateLimitingMiddleware {
   FastifyRateLimiter() { this = DataFlow::moduleImport("fastify-rate-limit") }
 }
+
+/**
+ * An options object with a `rateLimit` config passed to a Fastify shorthand route method,
+ * such as `fastify.post('/path', { config: { rateLimit: { ... } } }, handler)`.
+ */
+private class FastifyPerRouteRateLimit extends RateLimitingMiddleware {
+  FastifyPerRouteRateLimit() {
+    exists(Fastify::RouteSetup setup |
+      not setup.getMethodName() = ["route", "addHook"] and
+      setup.getNumArgument() >= 3 and
+      this.flowsTo(setup.getArgument(1))
+    |
+      exists(this.getAPropertySource("config").getAPropertySource("rateLimit"))
+      or
+      exists(this.getAPropertySource("rateLimit"))
+    )
+  }
+}
diff --git a/javascript/ql/src/change-notes/2026-04-13-fastify-per-route-rate-limit.md b/javascript/ql/src/change-notes/2026-04-13-fastify-per-route-rate-limit.md
new file mode 100644
index 000000000000..56d523885248
--- /dev/null
+++ b/javascript/ql/src/change-notes/2026-04-13-fastify-per-route-rate-limit.md
@@ -0,0 +1,5 @@
+---
+category: minorAnalysis
+---
+* The query `js/missing-rate-limiting` now takes Fastify per-route
+  rate limiting into account.
diff --git a/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/MissingRateLimiting.expected b/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/MissingRateLimiting.expected
index 3d7bc2954eba..8d197d6e37f6 100644
--- a/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/MissingRateLimiting.expected
+++ b/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/MissingRateLimiting.expected
@@ -9,3 +9,4 @@
 | tst.js:64:25:64:63 | functio ... req); } | This route handler performs $@, but is not rate-limited. | tst.js:64:46:64:60 | verifyUser(req) | authorization |
 | tst.js:76:25:76:53 | catchAs ... ndler1) | This route handler performs $@, but is not rate-limited. | tst.js:14:40:14:46 | login() | authorization |
 | tst.js:88:24:88:40 | expensiveHandler1 | This route handler performs $@, but is not rate-limited. | tst.js:14:40:14:46 | login() | authorization |
+| tst.js:112:28:112:44 | expensiveHandler1 | This route handler performs $@, but is not rate-limited. | tst.js:14:40:14:46 | login() | authorization |
diff --git a/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/tst.js b/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/tst.js
index 4f778afef684..5b4312bbbe0e 100644
--- a/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/tst.js
+++ b/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/tst.js
@@ -88,3 +88,25 @@ const fastifyApp = require('fastify')();
 fastifyApp.get('/foo', expensiveHandler1); // $ Alert
 fastifyApp.register(require('fastify-rate-limit'));
 fastifyApp.get('/bar', expensiveHandler1);
+
+// Fastify per-route rate limiting via config.rateLimit
+const fastifyApp2 = require('fastify')();
+fastifyApp2.register(require('@fastify/rate-limit'));
+
+fastifyApp2.post('/login', {
+  config: {
+    rateLimit: {
+      max: 3,
+      timeWindow: '1 minute'
+    }
+  }
+}, expensiveHandler1); // OK - has per-route rateLimit config
+
+fastifyApp2.post('/signup', {
+  rateLimit: {
+    max: 5,
+    timeWindow: '1 minute'
+  }
+}, expensiveHandler1); // OK - has per-route rateLimit directly in options
+
+fastifyApp2.post('/other', expensiveHandler1); // $ Alert - no rate limiting