diff --git a/pcsx2/Pcsx2Config.cpp b/pcsx2/Pcsx2Config.cpp
index 1376c9cc95..02a7ecde14 100644
--- a/pcsx2/Pcsx2Config.cpp
+++ b/pcsx2/Pcsx2Config.cpp
@@ -322,7 +322,6 @@ bool Pcsx2Config::GSOptions::operator==(const GSOptions& right) const
 
 		OpEqu(FrameSkipEnable) &&
 		OpEqu(FrameLimitEnable) &&
-		OpEqu(VsyncEnable) &&
 
 		OpEqu(FramesToDraw) &&
 		OpEqu(FramesToSkip) &&
@@ -343,6 +342,8 @@ bool Pcsx2Config::GSOptions::OptionsAreEqual(const GSOptions& right) const
 	return (
 		   OpEqu(bitset) &&
 
+		   OpEqu(VsyncEnable) &&
+
 		   OpEqu(InterlaceMode) &&
 
 		   OpEqu(Zoom) &&
diff --git a/pcsx2/System/SysCoreThread.cpp b/pcsx2/System/SysCoreThread.cpp
index c436b6c0e9..c417dfdfcf 100644
--- a/pcsx2/System/SysCoreThread.cpp
+++ b/pcsx2/System/SysCoreThread.cpp
@@ -196,6 +196,7 @@ void SysCoreThread::ApplySettings(const Pcsx2Config& src)
 		// so, we should block here until GS has finished reinitializing, if needed.
 		Console.WriteLn("Applying GS settings...");
 		GetMTGS().ApplySettings();
+		GetMTGS().SetVSync(EmuConfig.GetEffectiveVsyncMode());
 		GetMTGS().WaitGS();
 	}
 }
@@ -239,6 +240,7 @@ void SysCoreThread::_reset_stuff_as_needed()
 
 	if (m_resetVsyncTimers)
 	{
+		GetMTGS().SetVSync(EmuConfig.GetEffectiveVsyncMode());
 		UpdateVSyncRate();
 		frameLimitReset();