diff --git a/superset-frontend/plugins/plugin-chart-echarts/src/components/Echart.tsx b/superset-frontend/plugins/plugin-chart-echarts/src/components/Echart.tsx
index e531db67eff..95e31481264 100644
--- a/superset-frontend/plugins/plugin-chart-echarts/src/components/Echart.tsx
+++ b/superset-frontend/plugins/plugin-chart-echarts/src/components/Echart.tsx
@@ -277,12 +277,24 @@ function Echart(
       chartRef.current?.setOption(themedEchartOptions, {
         notMerge,
         replaceMerge: notMerge ? undefined : ['series'],
-        lazyUpdate: isDashboardRefreshing,
+        // lazyUpdate defers render, causing tooltip crashes on stale shapes (#39247)
+        lazyUpdate: false,
       });
     }
     // eslint-disable-next-line react-hooks/exhaustive-deps -- isDashboardRefreshing intentionally excluded to prevent extra setOption calls
   }, [didMount, echartOptions, eventHandlers, zrEventHandlers, theme, vizType]);
 
+  // Clear tooltip on refresh start to avoid stale content (#39247)
+  useEffect(() => {
+    if (didMount && isDashboardRefreshing && chartRef.current) {
+      chartRef.current.dispatchAction({ type: 'hideTip' });
+      chartRef.current.dispatchAction({
+        type: 'updateAxisPointer',
+        currTrigger: 'leave',
+      });
+    }
+  }, [didMount, isDashboardRefreshing]);
+
   useEffect(() => () => chartRef.current?.dispose(), []);
 
   // highlighting