diff --git a/src/drivers/kinetis/drv_io_timer.c b/src/drivers/kinetis/drv_io_timer.c
index 7a0b2dad4e..b049f6c2a7 100644
--- a/src/drivers/kinetis/drv_io_timer.c
+++ b/src/drivers/kinetis/drv_io_timer.c
@@ -456,11 +456,16 @@ static int allocate_channel(unsigned channel, io_timer_channel_mode_t mode)
 static int timer_set_rate(unsigned timer, unsigned rate)
 {
 
+	irqstate_t flags = px4_enter_critical_section();
+
+	uint32_t save = rSC(timer);
+	rSC(timer) = save & ~(FTM_SC_CLKS_MASK);
+
 	/* configure the timer to update at the desired rate */
 	rMOD(timer) = (BOARD_PWM_FREQ / rate) - 1;
+	rSC(timer) = save;
 
-	/* generate an update event; reloads the counter and all registers */
-	rSYNC(timer) = FTM_SYNC;
+	px4_leave_critical_section(flags);
 
 	return 0;
 }