diff --git a/Source/Core/Core/HW/CPU.cpp b/Source/Core/Core/HW/CPU.cpp
index 32b41ee06457..f2c805588666 100644
--- a/Source/Core/Core/HW/CPU.cpp
+++ b/Source/Core/Core/HW/CPU.cpp
@@ -81,11 +81,17 @@ void CPUManager::StartTimePlayedTimer()
     auto curr_time = timer.now();
 
     // Check that emulation is not paused
+    // If the emulation is paused, wait for SetStepping() to reactivate
     if (m_state == State::Running)
     {
       auto diff_time = std::chrono::duration_cast<std::chrono::milliseconds>(curr_time - prev_time);
       time_played.AddTime(diff_time);
     }
+    else if (m_state == State::Stepping)
+    {
+      m_time_played_finish_sync.Wait();
+      curr_time = timer.now();
+    }
 
     prev_time = curr_time;
 
@@ -313,6 +319,7 @@ void CPUManager::SetStepping(bool stepping)
   else if (SetStateLocked(State::Running))
   {
     m_state_cpu_cvar.notify_one();
+    m_time_played_finish_sync.Set();
     RunAdjacentSystems(true);
   }
 }