diff --git a/pcsx2/gui/AppMain.cpp b/pcsx2/gui/AppMain.cpp
index 323c434516..8055f40823 100644
--- a/pcsx2/gui/AppMain.cpp
+++ b/pcsx2/gui/AppMain.cpp
@@ -1089,6 +1089,7 @@ protected:
 
 		CoreThread.ResetQuick();
 		symbolMap.Clear();
+		CBreakPoints::SetSkipFirst(0);
 
 		CDVDsys_SetFile(CDVD_SourceType::Iso, g_Conf->CurrentIso );
 		if( m_UseCDVDsrc )