diff --git a/pcsx2-gsrunner/Main.cpp b/pcsx2-gsrunner/Main.cpp
index cfb61e74cb0f5..ffa89abc04df8 100644
--- a/pcsx2-gsrunner/Main.cpp
+++ b/pcsx2-gsrunner/Main.cpp
@@ -707,7 +707,7 @@ int main(int argc, char* argv[])
 	return EXIT_SUCCESS;
 }
 
-void Host::VSyncOnCPUThread()
+void Host::PumpMessagesOnCPUThread()
 {
 	// update GS thread copy of frame number
 	MTGS::RunOnGSThread([frame_number = GSDumpReplayer::GetFrameNumber()]() { s_dump_frame_number = frame_number; });
diff --git a/pcsx2-qt/QtHost.cpp b/pcsx2-qt/QtHost.cpp
index ef3d00bd1f705..8fc16565d14dc 100644
--- a/pcsx2-qt/QtHost.cpp
+++ b/pcsx2-qt/QtHost.cpp
@@ -1122,7 +1122,7 @@ void Host::OnCreateMemoryCardOpenRequested()
 	emit g_emu_thread->onCreateMemoryCardOpenRequested();
 }
 
-void Host::VSyncOnCPUThread()
+void Host::PumpMessagesOnCPUThread()
 {
 	g_emu_thread->getEventLoop()->processEvents(QEventLoop::AllEvents);
 }
diff --git a/pcsx2/Counters.cpp b/pcsx2/Counters.cpp
index 47e8fbb40117c..062aa1746613e 100644
--- a/pcsx2/Counters.cpp
+++ b/pcsx2/Counters.cpp
@@ -498,6 +498,9 @@ static __fi void VSyncStart(u32 sCycle)
 
 	gsPostVsyncStart(); // MUST be after framelimit; doing so before causes funk with frame times!
 
+	// Poll input after MTGS frame push, just in case it has to stall to catch up.
+	VMManager::Internal::PollInputOnCPUThread();
+
 	if (EmuConfig.Trace.Enabled && EmuConfig.Trace.EE.m_EnableAll)
 		SysTrace.EE.Counters.Write("    ================  EE COUNTER VSYNC START (frame: %d)  ================", g_FrameCount);
 
diff --git a/pcsx2/VMManager.cpp b/pcsx2/VMManager.cpp
index c04dc869601b4..a7f6be821e852 100644
--- a/pcsx2/VMManager.cpp
+++ b/pcsx2/VMManager.cpp
@@ -2484,11 +2484,13 @@ void VMManager::Internal::VSyncOnCPUThread()
 	Achievements::FrameUpdate();
 
 	PollDiscordPresence();
+}
 
+void VMManager::Internal::PollInputOnCPUThread()
+{
+	Host::PumpMessagesOnCPUThread();
 	InputManager::PollSources();
 
-	Host::VSyncOnCPUThread();
-
 	if (EmuConfig.EnableRecordingTools)
 	{
 		// This code is called _before_ Counter's vsync end, and _after_ vsync start
diff --git a/pcsx2/VMManager.h b/pcsx2/VMManager.h
index 5090a9929869f..9afa4470938b7 100644
--- a/pcsx2/VMManager.h
+++ b/pcsx2/VMManager.h
@@ -272,6 +272,7 @@ namespace VMManager
 		void ELFLoadingOnCPUThread(std::string elf_path);
 		void EntryPointCompilingOnCPUThread();
 		void VSyncOnCPUThread();
+		void PollInputOnCPUThread();
 	} // namespace Internal
 } // namespace VMManager
 
@@ -317,5 +318,5 @@ namespace Host
 		const std::string& disc_serial, u32 disc_crc, u32 current_crc);
 
 	/// Provided by the host; called once per frame at guest vsync.
-	void VSyncOnCPUThread();
+	void PumpMessagesOnCPUThread();
 } // namespace Host
diff --git a/tests/ctest/core/StubHost.cpp b/tests/ctest/core/StubHost.cpp
index 23ea03336f510..b6f66e5db1a57 100644
--- a/tests/ctest/core/StubHost.cpp
+++ b/tests/ctest/core/StubHost.cpp
@@ -169,7 +169,7 @@ void Host::RequestVMShutdown(bool allow_confirm, bool allow_save_state, bool def
 {
 }
 
-void Host::VSyncOnCPUThread()
+void Host::PumpMessagesOnCPUThread()
 {
 }