diff --git a/cmd/prometheus/main.go b/cmd/prometheus/main.go
index 0dd07e637..7e153bc32 100644
--- a/cmd/prometheus/main.go
+++ b/cmd/prometheus/main.go
@@ -102,7 +102,6 @@ type flagConfig struct {
 
 	localStoragePath    string
 	notifier            notifier.Options
-	notifierTimeout     model.Duration
 	forGracePeriod      model.Duration
 	outageTolerance     model.Duration
 	resendDelay         model.Duration
@@ -275,8 +274,8 @@ func main() {
 	a.Flag("alertmanager.notification-queue-capacity", "The capacity of the queue for pending Alertmanager notifications.").
 		Default("10000").IntVar(&cfg.notifier.QueueCapacity)
 
-	a.Flag("alertmanager.timeout", "Timeout for sending alerts to Alertmanager.").
-		Default("10s").SetValue(&cfg.notifierTimeout)
+	// TODO: Remove in Prometheus 3.0.
+	alertmanagerTimeout := a.Flag("alertmanager.timeout", "[DEPRECATED] This flag has no effect.").Hidden().String()
 
 	a.Flag("query.lookback-delta", "The maximum lookback duration for retrieving metrics during expression evaluations and federation.").
 		Default("5m").SetValue(&cfg.lookbackDelta)
@@ -321,6 +320,10 @@ func main() {
 		os.Exit(2)
 	}
 
+	if *alertmanagerTimeout != "" {
+		level.Warn(logger).Log("msg", "The flag --alertmanager.timeout has no effect and will be removed in the future.")
+	}
+
 	// Throw error for invalid config before starting other components.
 	if _, err := config.LoadFile(cfg.configFile); err != nil {
 		level.Error(logger).Log("msg", fmt.Sprintf("Error loading config (--config.file=%s)", cfg.configFile), "err", err)