diff --git a/Marlin/src/HAL/TEENSY40_41/timers.h b/Marlin/src/HAL/TEENSY40_41/timers.h
index 64f9112a57..98a852ee57 100644
--- a/Marlin/src/HAL/TEENSY40_41/timers.h
+++ b/Marlin/src/HAL/TEENSY40_41/timers.h
@@ -89,8 +89,16 @@ void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency);
 
 FORCE_INLINE static void HAL_timer_set_compare(const uint8_t timer_num, const hal_timer_t compare) {
   switch (timer_num) {
-    case MF_TIMER_STEP: GPT1_OCR1 = compare - 1; break;
-    case MF_TIMER_TEMP: GPT2_OCR1 = compare - 1; break;
+    case MF_TIMER_STEP:
+      GPT1_CR |= GPT_CR_FRR;    // Free Run Mode (setting OCRx preserves CNT)
+      GPT1_OCR1 = compare - 1;
+      GPT1_CR &= ~GPT_CR_FRR;   // Reset Mode (CNT resets on trigger)
+      break;
+    case MF_TIMER_TEMP:
+      GPT2_CR |= GPT_CR_FRR;    // Free Run Mode (setting OCRx preserves CNT)
+      GPT2_OCR1 = compare - 1;
+      GPT2_CR &= ~GPT_CR_FRR;   // Reset Mode (CNT resets on trigger)
+      break;
   }
 }