diff --git a/Marlin/src/module/temperature.cpp b/Marlin/src/module/temperature.cpp
index 46b88b10f..5756eda8a 100644
--- a/Marlin/src/module/temperature.cpp
+++ b/Marlin/src/module/temperature.cpp
@@ -1171,6 +1171,13 @@ void Temperature::init() {
     #endif
   #endif
 
+  #if ENABLED(USE_CONTROLLER_FAN)
+    SET_OUTPUT(CONTROLLER_FAN_PIN);
+    #if ENABLED(FAST_PWM_FAN)
+      setPwmFrequency(CONTROLLER_FAN_PIN, 1); // No prescaling. Pwm frequency = F_CPU/256/8
+    #endif
+  #endif
+
   #if ENABLED(HEATER_0_USES_MAX6675)
 
     OUT_WRITE(SCK_PIN, LOW);