diff --git a/pcsx2/DebugTools/Breakpoints.cpp b/pcsx2/DebugTools/Breakpoints.cpp
index 34b7fa738817b..03046b2d81027 100644
--- a/pcsx2/DebugTools/Breakpoints.cpp
+++ b/pcsx2/DebugTools/Breakpoints.cpp
@@ -377,6 +377,14 @@ u32 CBreakPoints::CheckSkipFirst(BreakPointCpu cpu, u32 cmpPc)
 	return 0;
 }
 
+void CBreakPoints::ClearSkipFirst()
+{
+	breakSkipFirstAtEE_ = 0;
+	breakSkipFirstTicksEE_ = 0;
+	breakSkipFirstAtIop_ = 0;
+	breakSkipFirstTicksIop_ = 0;
+}
+
 const std::vector<MemCheck> CBreakPoints::GetMemCheckRanges()
 {
 	std::vector<MemCheck> ranges = memChecks_;
diff --git a/pcsx2/DebugTools/Breakpoints.h b/pcsx2/DebugTools/Breakpoints.h
index 667552d9a9e9f..141c6442dee1c 100644
--- a/pcsx2/DebugTools/Breakpoints.h
+++ b/pcsx2/DebugTools/Breakpoints.h
@@ -138,6 +138,7 @@ class CBreakPoints
 
 	static void SetSkipFirst(BreakPointCpu cpu, u32 pc);
 	static u32 CheckSkipFirst(BreakPointCpu cpu, u32 pc);
+	static void ClearSkipFirst();
 
 	// Includes uncached addresses.
 	static const std::vector<MemCheck> GetMemCheckRanges();
diff --git a/pcsx2/R5900.cpp b/pcsx2/R5900.cpp
index c353a0c25429f..cd2ba9bcf17f7 100644
--- a/pcsx2/R5900.cpp
+++ b/pcsx2/R5900.cpp
@@ -96,6 +96,8 @@ void cpuReset()
 	g_eeloadMain = 0;
 	g_eeloadExec = 0;
 	g_osdsys_str = 0;
+
+	CBreakPoints::ClearSkipFirst();
 }
 
 __ri void cpuException(u32 code, u32 bd)