diff --git a/apps/web/src/components/chat/MessagesTimeline.test.tsx b/apps/web/src/components/chat/MessagesTimeline.test.tsx
index ea6cda9b6208..80ebaa96a307 100644
--- a/apps/web/src/components/chat/MessagesTimeline.test.tsx
+++ b/apps/web/src/components/chat/MessagesTimeline.test.tsx
@@ -1,5 +1,5 @@
 import { CheckpointRef, EnvironmentId, MessageId, TurnId } from "@t3tools/contracts";
-import { createRef, type ReactNode, type Ref } from "react";
+import { type ComponentProps, createRef, type ReactNode, type Ref } from "react";
 import { renderToStaticMarkup } from "react-dom/server";
 import { beforeAll, describe, expect, it, vi } from "vite-plus/test";
 import type { LegendListRef } from "@legendapp/list/react";
@@ -125,6 +125,19 @@ vi.mock("@pierre/diffs/react", () => {
   return { FileDiff: MockFileDiff };
 });
 
+vi.mock("../ui/tooltip", async (importOriginal) => {
+  const actual = await importOriginal<typeof import("../ui/tooltip")>();
+
+  return {
+    ...actual,
+    TooltipScrollDismissProvider: ({
+      children,
+    }: ComponentProps<typeof actual.TooltipScrollDismissProvider>) => (
+      <div data-tooltip-scroll-dismiss="enabled">{children}</div>
+    ),
+  };
+});
+
 function matchMedia() {
   return {
     matches: false,
@@ -236,6 +249,17 @@ function buildAssistantTimelineEntry(text: string) {
 }
 
 describe("MessagesTimeline", () => {
+  it("enables tooltip scroll dismissal in the timeline", () => {
+    const markup = renderToStaticMarkup(
+      <MessagesTimeline
+        {...buildProps()}
+        timelineEntries={[buildAssistantTimelineEntry("[Link](https://example.com)")]}
+      />,
+    );
+
+    expect(markup).toContain('data-tooltip-scroll-dismiss="enabled"');
+  });
+
   it("renders the worked-for row at assistant response text size", () => {
     const turnId = TurnId.make("turn-with-fold");
     const assistantEntry = buildAssistantTimelineEntry("Done.");
diff --git a/apps/web/src/components/chat/MessagesTimeline.tsx b/apps/web/src/components/chat/MessagesTimeline.tsx
index 6d89140d1105..f1aa5878fd84 100644
--- a/apps/web/src/components/chat/MessagesTimeline.tsx
+++ b/apps/web/src/components/chat/MessagesTimeline.tsx
@@ -90,7 +90,8 @@ import {
   type TimelineLatestTurn,
 } from "./MessagesTimeline.logic";
 import { TerminalContextInlineChip } from "./TerminalContextInlineChip";
-import { Tooltip, TooltipPopup, TooltipTrigger } from "../ui/tooltip";
+import { Tooltip, TooltipPopup, TooltipScrollDismissProvider, TooltipTrigger } from "../ui/tooltip";
+import { createTooltipScrollDismissController } from "../ui/tooltipScrollDismiss";
 import {
   deriveDisplayedUserMessageState,
   type ParsedTerminalContextEntry,
@@ -283,6 +284,7 @@ export const MessagesTimeline = memo(function MessagesTimeline({
   const [expandedWorkGroupIds, setExpandedWorkGroupIds] = useState<ReadonlySet<string>>(new Set());
   const [disclosureToggleSettling, setDisclosureToggleSettling] = useState(false);
   const [minimapStripMap] = useState(() => new Map<string, HTMLSpanElement>());
+  const tooltipScrollDismissController = useMemo(createTooltipScrollDismissController, []);
   const disclosureAnchorKeyRef = useRef<string | null>(null);
   const disclosureSettleFrameRef = useRef<number | null>(null);
   const disclosureSettleSecondFrameRef = useRef<number | null>(null);
@@ -438,7 +440,7 @@ export const MessagesTimeline = memo(function MessagesTimeline({
     return config ? { ...config, onReady: handleAnchorReady } : undefined;
   }, [anchorMessageId, handleAnchorReady, rows]);
 
-  const handleScroll = useCallback(() => {
+  const updateTimelineScrollState = useCallback(() => {
     const state = listRef.current?.getState?.();
     const isAtEnd = resolveTimelineIsAtEnd(state, contentInsetEndAdjustment);
     if (isAtEnd !== undefined) {
@@ -468,10 +470,15 @@ export const MessagesTimeline = memo(function MessagesTimeline({
     }
   }, [contentInsetEndAdjustment, listRef, minimapItems, minimapStripMap, onIsAtEndChange]);
 
+  const handleScroll = useCallback(() => {
+    tooltipScrollDismissController.dismissHoveredTooltip();
+    updateTimelineScrollState();
+  }, [tooltipScrollDismissController, updateTimelineScrollState]);
+
   useEffect(() => {
-    const frame = requestAnimationFrame(handleScroll);
+    const frame = requestAnimationFrame(updateTimelineScrollState);
     return () => cancelAnimationFrame(frame);
-  }, [handleScroll, rows.length]);
+  }, [rows.length, updateTimelineScrollState]);
 
   useEffect(() => {
     if (!timelineViewportElement) {
@@ -565,7 +572,7 @@ export const MessagesTimeline = memo(function MessagesTimeline({
     );
   }
 
-  return (
+  const timeline = (
     <TimelineRowCtx value={sharedState}>
       <TimelineRowActivityCtx value={activityState}>
         <div ref={setTimelineViewportElement} className="relative h-full min-h-0">
@@ -623,6 +630,14 @@ export const MessagesTimeline = memo(function MessagesTimeline({
       </TimelineRowActivityCtx>
     </TimelineRowCtx>
   );
+
+  return (
+    <TooltipScrollDismissProvider
+      onTriggerHoverChange={tooltipScrollDismissController.setHoveredTooltip}
+    >
+      {timeline}
+    </TooltipScrollDismissProvider>
+  );
 });
 
 function keyExtractor(item: MessagesTimelineRow) {
diff --git a/apps/web/src/components/ui/tooltip.test.tsx b/apps/web/src/components/ui/tooltip.test.tsx
new file mode 100644
index 000000000000..d5cc887fd24c
--- /dev/null
+++ b/apps/web/src/components/ui/tooltip.test.tsx
@@ -0,0 +1,125 @@
+import { type ComponentProps, Fragment, type ReactNode } from "react";
+import { renderToStaticMarkup } from "react-dom/server";
+import { describe, expect, it, vi } from "vite-plus/test";
+
+vi.mock("@base-ui/react/tooltip", () => {
+  function Positioner({
+    children,
+    className,
+    ...props
+  }: ComponentProps<"div"> & { children?: ReactNode }) {
+    return (
+      <div className={className} {...props}>
+        {children}
+      </div>
+    );
+  }
+
+  function Element({ children, ...props }: ComponentProps<"div"> & { children?: ReactNode }) {
+    return <div {...props}>{children}</div>;
+  }
+
+  return {
+    Tooltip: {
+      createHandle: () => ({}),
+      Provider: Fragment,
+      Root: Fragment,
+      Trigger: Element,
+      Portal: Fragment,
+      Positioner,
+      Popup: Element,
+      Viewport: Element,
+    },
+  };
+});
+
+import { TooltipPopup, TooltipScrollDismissProvider } from "./tooltip";
+import { createTooltipScrollDismissController } from "./tooltipScrollDismiss";
+
+function createFakeTooltipTrigger() {
+  const ownerDocument = {
+    activeElement: null as Element | null,
+  };
+  const descendants = new Set<Node>();
+  const trigger = {
+    ownerDocument,
+    contains(node: Node | null) {
+      return node === trigger || (node !== null && descendants.has(node));
+    },
+  } as unknown as HTMLElement;
+
+  return { descendants, ownerDocument, trigger };
+}
+
+describe("tooltip layering", () => {
+  it("keeps global tooltips above dropdowns", () => {
+    const html = renderToStaticMarkup(<TooltipPopup>Global tooltip</TooltipPopup>);
+
+    expect(html).toContain("z-[140]");
+  });
+
+  it("keeps timeline tooltips above chat chrome", () => {
+    const html = renderToStaticMarkup(
+      <TooltipScrollDismissProvider onTriggerHoverChange={() => {}}>
+        <TooltipPopup>Timeline tooltip</TooltipPopup>
+      </TooltipScrollDismissProvider>,
+    );
+
+    expect(html).toContain("z-[140]");
+    expect(html).not.toContain("z-[15]");
+  });
+});
+
+describe("tooltip scroll dismissal", () => {
+  it("dismisses the hovered tooltip once when its content scrolls", () => {
+    const controller = createTooltipScrollDismissController();
+    const { trigger } = createFakeTooltipTrigger();
+    const dismiss = vi.fn();
+
+    controller.setHoveredTooltip({ trigger, dismiss });
+    controller.dismissHoveredTooltip();
+    controller.dismissHoveredTooltip();
+
+    expect(dismiss).toHaveBeenCalledOnce();
+  });
+
+  it("keeps a focused tooltip open when its content scrolls", () => {
+    const controller = createTooltipScrollDismissController();
+    const { ownerDocument, trigger } = createFakeTooltipTrigger();
+    const dismiss = vi.fn();
+    ownerDocument.activeElement = trigger;
+
+    controller.setHoveredTooltip({ trigger, dismiss });
+    controller.dismissHoveredTooltip();
+
+    expect(dismiss).not.toHaveBeenCalled();
+  });
+
+  it("dismisses a hovered tooltip on a later scroll after focus leaves", () => {
+    const controller = createTooltipScrollDismissController();
+    const { ownerDocument, trigger } = createFakeTooltipTrigger();
+    const dismiss = vi.fn();
+    ownerDocument.activeElement = trigger;
+
+    controller.setHoveredTooltip({ trigger, dismiss });
+    controller.dismissHoveredTooltip();
+    ownerDocument.activeElement = null;
+    controller.dismissHoveredTooltip();
+
+    expect(dismiss).toHaveBeenCalledOnce();
+  });
+
+  it("keeps a tooltip open when focus is within its trigger", () => {
+    const controller = createTooltipScrollDismissController();
+    const { descendants, ownerDocument, trigger } = createFakeTooltipTrigger();
+    const focusedChild = {} as Element;
+    const dismiss = vi.fn();
+    descendants.add(focusedChild);
+    ownerDocument.activeElement = focusedChild;
+
+    controller.setHoveredTooltip({ trigger, dismiss });
+    controller.dismissHoveredTooltip();
+
+    expect(dismiss).not.toHaveBeenCalled();
+  });
+});
diff --git a/apps/web/src/components/ui/tooltip.tsx b/apps/web/src/components/ui/tooltip.tsx
index 77b15a01e16b..fe49df261c07 100644
--- a/apps/web/src/components/ui/tooltip.tsx
+++ b/apps/web/src/components/ui/tooltip.tsx
@@ -1,15 +1,83 @@
 import { Tooltip as TooltipPrimitive } from "@base-ui/react/tooltip";
+import { createContext, type ReactNode, useCallback, useContext, useRef } from "react";
 
 import { cn } from "~/lib/utils";
+import type { HoveredTooltip } from "./tooltipScrollDismiss";
 
 const TooltipCreateHandle = TooltipPrimitive.createHandle;
 
+type TooltipScrollDismissContextValue = ((tooltip: HoveredTooltip | null) => void) | null;
+
+const TooltipScrollDismissContext = createContext<TooltipScrollDismissContextValue>(null);
+const TooltipDismissContext = createContext<(() => void) | null>(null);
+
+function TooltipScrollDismissProvider({
+  children,
+  onTriggerHoverChange,
+}: {
+  children: ReactNode;
+  onTriggerHoverChange: (tooltip: HoveredTooltip | null) => void;
+}) {
+  return (
+    <TooltipScrollDismissContext value={onTriggerHoverChange}>
+      {children}
+    </TooltipScrollDismissContext>
+  );
+}
+
 const TooltipProvider = TooltipPrimitive.Provider;
 
-const Tooltip = TooltipPrimitive.Root;
+function Tooltip<Payload>(props: TooltipPrimitive.Root.Props<Payload>) {
+  const onTriggerHoverChange = useContext(TooltipScrollDismissContext);
+
+  if (!onTriggerHoverChange) {
+    return <TooltipPrimitive.Root {...props} />;
+  }
+
+  return <TrackedTooltip {...props} />;
+}
+
+function TrackedTooltip<Payload>({ actionsRef, ...props }: TooltipPrimitive.Root.Props<Payload>) {
+  const localActionsRef = useRef<TooltipPrimitive.Root.Actions | null>(null);
+  const resolvedActionsRef = actionsRef ?? localActionsRef;
+  const dismiss = useCallback(() => resolvedActionsRef.current?.close(), [resolvedActionsRef]);
+
+  return (
+    <TooltipDismissContext value={dismiss}>
+      <TooltipPrimitive.Root actionsRef={resolvedActionsRef} {...props} />
+    </TooltipDismissContext>
+  );
+}
+
+function TooltipTrigger({ onMouseEnter, onMouseLeave, ...props }: TooltipPrimitive.Trigger.Props) {
+  const onTriggerHoverChange = useContext(TooltipScrollDismissContext);
+  const dismiss = useContext(TooltipDismissContext);
+
+  if (!onTriggerHoverChange || !dismiss) {
+    return (
+      <TooltipPrimitive.Trigger
+        data-slot="tooltip-trigger"
+        onMouseEnter={onMouseEnter}
+        onMouseLeave={onMouseLeave}
+        {...props}
+      />
+    );
+  }
 
-function TooltipTrigger(props: TooltipPrimitive.Trigger.Props) {
-  return <TooltipPrimitive.Trigger data-slot="tooltip-trigger" {...props} />;
+  return (
+    <TooltipPrimitive.Trigger
+      data-slot="tooltip-trigger"
+      onMouseEnter={(event) => {
+        onTriggerHoverChange({ trigger: event.currentTarget, dismiss });
+        onMouseEnter?.(event);
+      }}
+      onMouseLeave={(event) => {
+        onTriggerHoverChange(null);
+        onMouseLeave?.(event);
+      }}
+      {...props}
+    />
+  );
 }
 
 function TooltipPopup({
@@ -61,4 +129,11 @@ function TooltipPopup({
   );
 }
 
-export { TooltipCreateHandle, TooltipProvider, Tooltip, TooltipTrigger, TooltipPopup };
+export {
+  TooltipCreateHandle,
+  TooltipScrollDismissProvider,
+  TooltipProvider,
+  Tooltip,
+  TooltipTrigger,
+  TooltipPopup,
+};
diff --git a/apps/web/src/components/ui/tooltipScrollDismiss.ts b/apps/web/src/components/ui/tooltipScrollDismiss.ts
new file mode 100644
index 000000000000..eb96cae98ec7
--- /dev/null
+++ b/apps/web/src/components/ui/tooltipScrollDismiss.ts
@@ -0,0 +1,34 @@
+type HoveredTooltip = {
+  trigger: HTMLElement;
+  dismiss: () => void;
+};
+
+type TooltipScrollDismissController = {
+  setHoveredTooltip: (tooltip: HoveredTooltip | null) => void;
+  dismissHoveredTooltip: () => void;
+};
+
+function createTooltipScrollDismissController(): TooltipScrollDismissController {
+  let hoveredTooltip: HoveredTooltip | null = null;
+
+  return {
+    setHoveredTooltip(tooltip) {
+      hoveredTooltip = tooltip;
+    },
+    dismissHoveredTooltip() {
+      const tooltip = hoveredTooltip;
+
+      if (
+        tooltip === null ||
+        tooltip.trigger.contains(tooltip.trigger.ownerDocument.activeElement)
+      ) {
+        return;
+      }
+
+      hoveredTooltip = null;
+      tooltip.dismiss();
+    },
+  };
+}
+
+export { createTooltipScrollDismissController, type HoveredTooltip };