diff --git a/libraries/AP_HAL_AVR_SITL/SITL_State.cpp b/libraries/AP_HAL_AVR_SITL/SITL_State.cpp
index 34ef2aed55..928e40a549 100644
--- a/libraries/AP_HAL_AVR_SITL/SITL_State.cpp
+++ b/libraries/AP_HAL_AVR_SITL/SITL_State.cpp
@@ -215,7 +215,7 @@ void SITL_State::_sitl_setup(void)
 
     if (_synthetic_clock_mode) {
         // start with non-zero clock
-        hal.scheduler->stop_clock(100);
+        hal.scheduler->stop_clock(1);
     }
 
     // setup a pipe used to trigger loop to stop sleeping
diff --git a/libraries/AP_HAL_AVR_SITL/Scheduler.cpp b/libraries/AP_HAL_AVR_SITL/Scheduler.cpp
index 084d62c242..a8a5a06a69 100644
--- a/libraries/AP_HAL_AVR_SITL/Scheduler.cpp
+++ b/libraries/AP_HAL_AVR_SITL/Scheduler.cpp
@@ -317,6 +317,12 @@ void SITLScheduler::panic(const prog_char_t *errormsg) {
  */
 void SITLScheduler::stop_clock(uint64_t time_usec)
 {
+    if (time_usec == 1) {
+        // special case for initialisation in synthetic clock mode
+        stopped_clock_usec = time_usec;
+        return;
+    }
+
     if (stopped_clock_usec != 0) {
         /*
           wait until the main thread is waiting for us. This ensures