diff --git a/cpu/native/native_cpu.c b/cpu/native/native_cpu.c
index 2629e55df067..655562565e77 100644
--- a/cpu/native/native_cpu.c
+++ b/cpu/native/native_cpu.c
@@ -208,6 +208,8 @@ void isr_thread_yield(void)
 
 void thread_yield_higher(void)
 {
+    sched_context_switch_request = 1;
+
     if (_native_in_isr == 0) {
         ucontext_t *ctx = (ucontext_t *)(sched_active_thread->sp);
         _native_in_isr = 1;
@@ -224,9 +226,6 @@ void thread_yield_higher(void)
         }
         irq_enable();
     }
-    else {
-        sched_context_switch_request = 1;
-    }
 }
 
 void native_cpu_init(void)