diff --git a/src/stream/src/executor/flow_control.rs b/src/stream/src/executor/flow_control.rs
index b601cbde176c9..bab77215c30bf 100644
--- a/src/stream/src/executor/flow_control.rs
+++ b/src/stream/src/executor/flow_control.rs
@@ -40,8 +40,6 @@ type RateLimitConfig = Option<u32>;
 impl FlowControlExecutor {
     #[allow(clippy::too_many_arguments)]
     pub fn new(input: Box<dyn Executor>, rate_limit: Option<u32>) -> Self {
-        #[cfg(madsim)]
-        tracing::warn!("FlowControlExecutor rate limiter is disabled in madsim as it will spawn system threads");
         Self { input, rate_limit }
     }
 
@@ -52,6 +50,7 @@ impl FlowControlExecutor {
         let mut input_stream = input.execute();
         loop {
             match &rate_limit {
+                // If no rate limit, just need to handle cfg change.
                 None =>
                 {
                     #[for_await]
@@ -74,10 +73,13 @@ impl FlowControlExecutor {
                         }
                     }
                 }
+                // If rate limit, need to handle cfg change, and rate limit.
                 Some(rate_limit_value) => {
                     let quota = Quota::per_second(NonZeroU32::new(*rate_limit_value).unwrap());
                     let clock = MonotonicClock;
                     let rate_limiter = RateLimiter::direct_with_clock(quota, &clock);
+                    #[cfg(madsim)]
+                    let mut rate_limit_quota = *rate_limit_value;
                     #[for_await]
                     for msg in &mut input_stream {
                         let msg = msg?;
@@ -97,6 +99,25 @@ impl FlowControlExecutor {
                                         );
                                     }
                                 }
+                                #[cfg(madsim)]
+                                {
+                                    if rate_limit_quota < chunk.cardinality() as u32 {
+                                        tokio::time::sleep(std::time::Duration::from_secs(1));
+                                        rate_limit_quota = *rate_limit_value;
+                                        // If after reset, chunk cardinality is still greater than
+                                        // rate limit, we cannot apply rate limit to it.
+                                        if rate_limit_quota < chunk.cardinality() as u32 {
+                                            tracing::error!(
+                                                "Rate Limit {:?} smaller than chunk cardinality {n}",
+                                                rate_limit_value,
+                                            );
+                                        } else {
+                                            rate_limit_quota -= chunk.cardinality() as u32;
+                                        }
+                                    } else {
+                                        rate_limit_quota -= chunk.cardinality() as u32;
+                                    }
+                                }
                                 yield msg;
                             }
                             Message::Barrier(ref b) => {