diff --git a/src/core/core_timing.cpp b/src/core/core_timing.cpp
index d08c007bb..c85590d4c 100644
--- a/src/core/core_timing.cpp
+++ b/src/core/core_timing.cpp
@@ -159,6 +159,8 @@ void CoreTiming::UnscheduleEvent(const std::shared_ptr<EventType>& event_type,
         for (auto h : to_remove) {
             event_queue.erase(h);
         }
+
+        event_type->sequence_number++;
     }
 
     // Force any in-progress events to finish
@@ -202,9 +204,10 @@ std::optional<s64> CoreTiming::Advance() {
         const Event& evt = event_queue.top();
 
         if (const auto event_type{evt.type.lock()}) {
-            if (evt.reschedule_time == 0) {
-                const auto evt_time = evt.time;
+            const auto evt_time = evt.time;
+            const auto evt_sequence_num = event_type->sequence_number;
 
+            if (evt.reschedule_time == 0) {
                 event_queue.pop();
 
                 basic_lock.unlock();
@@ -217,10 +220,15 @@ std::optional<s64> CoreTiming::Advance() {
                 basic_lock.unlock();
 
                 const auto new_schedule_time{event_type->callback(
-                    evt.time, std::chrono::nanoseconds{GetGlobalTimeNs().count() - evt.time})};
+                    evt_time, std::chrono::nanoseconds{GetGlobalTimeNs().count() - evt_time})};
 
                 basic_lock.lock();
 
+                if (evt_sequence_num != event_type->sequence_number) {
+                    // Heap handle is invalidated after external modification.
+                    continue;
+                }
+
                 const auto next_schedule_time{new_schedule_time.has_value()
                                                   ? new_schedule_time.value().count()
                                                   : evt.reschedule_time};
diff --git a/src/core/core_timing.h b/src/core/core_timing.h
index d8cd599ee..7e4dff7f3 100644
--- a/src/core/core_timing.h
+++ b/src/core/core_timing.h
@@ -27,12 +27,15 @@ using TimedCallback = std::function<std::optional<std::chrono::nanoseconds>(
 /// Contains the characteristics of a particular event.
 struct EventType {
     explicit EventType(TimedCallback&& callback_, std::string&& name_)
-        : callback{std::move(callback_)}, name{std::move(name_)} {}
+        : callback{std::move(callback_)}, name{std::move(name_)}, sequence_number{0} {}
 
     /// The event's callback function.
     TimedCallback callback;
     /// A pointer to the name of the event.
     const std::string name;
+    /// A monotonic sequence number, incremented when this event is
+    /// changed externally.
+    size_t sequence_number;
 };
 
 enum class UnscheduleEventType {