diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd35ef4a9..3cd99d9e6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,8 @@
 
 - Hidden pre-compression snapshots no longer keep stale pin state or count toward the visible pinned-session quota (#3181).
 
+- Tool-call cards stay anchored when scrolling back through paginated history; legacy session-level tool-call indices are rebased to the returned message window and the browser refreshes tool-call anchors whenever a larger history window is loaded (#3120).
+
 
 ## [v0.51.171] — 2026-05-30 — Release EQ (stage-batch53 — tool-output card badge + Neon opt-in skin)
 
diff --git a/api/routes.py b/api/routes.py
index e30f2e9e6..90ca74c27 100644
--- a/api/routes.py
+++ b/api/routes.py
@@ -2276,7 +2276,13 @@ def _messages_include_tool_metadata(messages) -> bool:
 
 
 def _tool_calls_for_message_window(tool_calls, start_idx: int, message_count: int) -> list:
-    """Keep session-level tool calls that point into a returned message window."""
+    """Keep session-level tool calls that point into a returned message window.
+
+    ``assistant_msg_idx`` is stored in the full transcript coordinate space, but
+    the frontend renders the returned ``messages`` array from index 0. Rebase the
+    index into the returned window so legacy session-level tool cards still
+    anchor to their visible assistant turn after paginated loads.
+    """
     if not isinstance(tool_calls, list) or message_count <= 0:
         return []
     end_idx = start_idx + message_count
@@ -2288,7 +2294,9 @@ def _tool_calls_for_message_window(tool_calls, start_idx: int, message_count: in
         if isinstance(assistant_idx, bool) or not isinstance(assistant_idx, int):
             continue
         if start_idx <= assistant_idx < end_idx:
-            filtered.append(tool_call)
+            rebased = dict(tool_call)
+            rebased["assistant_msg_idx"] = assistant_idx - start_idx
+            filtered.append(rebased)
     return filtered
 
 
diff --git a/static/sessions.js b/static/sessions.js
index 76b9c7dc2..1cd17da3f 100644
--- a/static/sessions.js
+++ b/static/sessions.js
@@ -1310,6 +1310,21 @@ let _messagesTruncated = false;
 // Older messages are loaded on-demand via _loadOlderMessages().
 const _INITIAL_MSG_LIMIT = 30;
 
+function _syncToolCallsForLoadedMessages(messages, sessionToolCalls){
+  const msgs=Array.isArray(messages)?messages:[];
+  const hasMessageToolMetadata=msgs.some(m=>{
+    if(!m) return false;
+    const hasTc=Array.isArray(m.tool_calls)&&m.tool_calls.length>0;
+    const hasTu=Array.isArray(m.content)&&m.content.some(p=>p&&p.type==='tool_use');
+    return hasTc||hasTu;
+  });
+  if(!hasMessageToolMetadata&&Array.isArray(sessionToolCalls)&&sessionToolCalls.length){
+    S.toolCalls=sessionToolCalls.map(tc=>({...tc,done:true}));
+  }else{
+    S.toolCalls=[];
+  }
+}
+
 async function _ensureMessagesLoaded(sid) {
   // Already have messages? (e.g. from INFLIGHT restore path, already set)
   if (S.messages && S.messages.length > 0 && S.messages[0] && S.messages[0].role) {
@@ -1327,17 +1342,7 @@ async function _ensureMessagesLoaded(sid) {
   // toast on every mobile message (SSE/visibility events trigger this reload path
   // more aggressively on mobile).
   let msgs = (data.session.messages || []).filter(m => m && m.role);
-  // Check for tool-call metadata on messages (for tool-call card rendering)
-  const hasMessageToolMetadata = msgs.some(m => {
-    const hasTc = Array.isArray(m.tool_calls) && m.tool_calls.length > 0;
-    const hasTu = Array.isArray(m.content) && m.content.some(p => p && p.type === 'tool_use');
-    return hasTc || hasTu;
-  });
-  if (!hasMessageToolMetadata && data.session.tool_calls && data.session.tool_calls.length) {
-    S.toolCalls = data.session.tool_calls.map(tc => ({...tc, done: true}));
-  } else {
-    S.toolCalls = [];
-  }
+  _syncToolCallsForLoadedMessages(msgs, data.session.tool_calls);
   clearLiveToolCards();
   // #3018: preserve client-side ephemeral turn fields (_turnUsage, _turnDuration,
   // _turnTps, _gatewayRouting, _statusCard) across the loadSession replace.
@@ -1500,6 +1505,7 @@ async function _loadOlderMessages() {
     const container = $('messages');
     const prevScrollH = container ? container.scrollHeight : 0;
     S.messages = nextMessages;
+    _syncToolCallsForLoadedMessages(nextMessages, responseSession.tool_calls);
     // renderMessages() windows long transcripts from the end. If we do not
     // expand that window before rendering, the newly prepended page stays
     // hidden and the "hidden" counter rises while the viewport appears stuck.
@@ -1584,6 +1590,7 @@ async function _ensureAllMessagesLoaded() {
     S.messages = msgs;
     _messagesTruncated = false;
     _oldestIdx = 0;
+    _syncToolCallsForLoadedMessages(msgs, data.session.tool_calls);
     if (S.session && S.session.session_id === sid) {
       S.session.message_count = Number(data.session.message_count || msgs.length);
     }
diff --git a/tests/test_issue401.py b/tests/test_issue401.py
index 174645e43..ab8b3c260 100644
--- a/tests/test_issue401.py
+++ b/tests/test_issue401.py
@@ -28,10 +28,10 @@ def test_loadsession_preserves_tool_rows():
 
 def test_loadsession_uses_session_toolcalls_only_as_fallback():
     """Session summaries are the fallback, not the primary reload source."""
-    assert ("if(!hasMessageToolMetadata&&data.session.tool_calls&&data.session.tool_calls.length)" in SESSIONS_JS or
-            "if (!hasMessageToolMetadata && data.session.tool_calls && data.session.tool_calls.length)" in SESSIONS_JS)
-    assert ("S.toolCalls=(data.session.tool_calls||[]).map(tc=>({...tc,done:true}));" in SESSIONS_JS or
-            "S.toolCalls = data.session.tool_calls.map(tc => ({...tc, done: true}));" in SESSIONS_JS)
+    assert "function _syncToolCallsForLoadedMessages(messages, sessionToolCalls)" in SESSIONS_JS
+    assert "if(!hasMessageToolMetadata&&Array.isArray(sessionToolCalls)&&sessionToolCalls.length)" in SESSIONS_JS
+    assert "windowOffset" not in SESSIONS_JS
+    assert "copy.assistant_msg_idx=idx-offset;" not in SESSIONS_JS
     assert "S.toolCalls=[];" in SESSIONS_JS
 
 
@@ -114,3 +114,27 @@ def test_reload_uses_session_summary_when_messages_have_no_tool_metadata():
     assert result["has_metadata"] is False
     assert result["fallback_len"] == 1
     assert result["done_flag"] is True
+
+
+def test_rebased_legacy_toolcalls_stay_distinct_in_paged_window():
+    """Backend-rebased legacy tool calls must not be rebased a second time."""
+    result = _run_js("""
+        const messages = [
+            { role: 'assistant', content: 'first legacy page row' },
+            { role: 'assistant', content: 'second legacy page row' }
+        ];
+        const sessionToolCalls = [
+            { name: 'first_tool', assistant_msg_idx: 0, snippet: 'first' },
+            { name: 'second_tool', assistant_msg_idx: 1, snippet: 'second' }
+        ];
+        const loaded = loadSessionShape(messages, sessionToolCalls);
+        const renderedRawIdxs = messages.map((_, idx) => idx);
+        process.stdout.write(JSON.stringify({
+            indices: loaded.toolCalls.map(tc => tc.assistant_msg_idx),
+            distinct_indices: new Set(loaded.toolCalls.map(tc => tc.assistant_msg_idx)).size,
+            anchors_visible: loaded.toolCalls.every(tc => renderedRawIdxs.includes(tc.assistant_msg_idx))
+        }));
+    """)
+    assert result["indices"] == [0, 1]
+    assert result["distinct_indices"] == 2
+    assert result["anchors_visible"] is True
diff --git a/tests/test_session_tail_payload.py b/tests/test_session_tail_payload.py
index da6cad85f..dee5600c4 100644
--- a/tests/test_session_tail_payload.py
+++ b/tests/test_session_tail_payload.py
@@ -92,7 +92,10 @@ def test_tail_window_keeps_only_visible_session_tool_calls_for_legacy_messages_w
     payload = _invoke(session)
 
     assert payload["messages"] == [session.messages[-1]]
-    assert payload["tool_calls"] == [session.tool_calls[-1]]
+    assert payload["tool_calls"] == [
+        {"name": "visible-tool", "snippet": "visible snippet", "assistant_msg_idx": 0}
+    ]
+    assert session.tool_calls[-1]["assistant_msg_idx"] == 1
 
 
 def test_full_load_keeps_all_session_tool_calls_for_legacy_messages_without_metadata():
@@ -114,11 +117,12 @@ def test_msg_before_window_keeps_only_that_page_session_tool_calls():
     session = _FakeSession([
         {"role": "user", "content": "first"},
         {"role": "assistant", "content": "second legacy message"},
-        {"role": "user", "content": "third"},
+        {"role": "assistant", "content": "third legacy message"},
         {"role": "assistant", "content": "fourth legacy message"},
     ])
     session.tool_calls = [
         {"name": "first-page-tool", "snippet": "kept", "assistant_msg_idx": 1},
+        {"name": "second-page-tool", "snippet": "also kept", "assistant_msg_idx": 2},
         {"name": "tail-tool", "snippet": "not in page", "assistant_msg_idx": 3},
         {"name": "unindexed-tool", "snippet": "cannot place"},
     ]
@@ -129,5 +133,10 @@ def test_msg_before_window_keeps_only_that_page_session_tool_calls():
     )
 
     assert payload["messages"] == session.messages[1:3]
-    assert payload["tool_calls"] == [session.tool_calls[0]]
+    assert payload["tool_calls"] == [
+        {"name": "first-page-tool", "snippet": "kept", "assistant_msg_idx": 0},
+        {"name": "second-page-tool", "snippet": "also kept", "assistant_msg_idx": 1},
+    ]
+    assert session.tool_calls[0]["assistant_msg_idx"] == 1
+    assert session.tool_calls[1]["assistant_msg_idx"] == 2
     assert payload["_messages_offset"] == 1
diff --git a/tests/test_tool_call_history_paging.py b/tests/test_tool_call_history_paging.py
new file mode 100644
index 000000000..23cf9b344
--- /dev/null
+++ b/tests/test_tool_call_history_paging.py
@@ -0,0 +1,28 @@
+from pathlib import Path
+
+
+ROOT = Path(__file__).resolve().parents[1]
+SESSIONS_JS = (ROOT / "static" / "sessions.js").read_text(encoding="utf-8")
+
+
+def test_sessions_js_resyncs_tool_calls_after_history_window_replacement():
+    """History paging replaces S.messages with a larger window.
+
+    Legacy sessions keep tool card data in session.tool_calls, so that side data
+    must be refreshed alongside the message window. Otherwise renderMessages()
+    can keep stale anchors and show unloaded/thinking placeholders while the
+    user scrolls through history.
+    """
+    assert "function _syncToolCallsForLoadedMessages(messages, sessionToolCalls)" in SESSIONS_JS
+    assert "_syncToolCallsForLoadedMessages(msgs, data.session.tool_calls);" in SESSIONS_JS
+    assert "S.messages = nextMessages;\n    _syncToolCallsForLoadedMessages(nextMessages, responseSession.tool_calls);" in SESSIONS_JS
+    assert "S.messages = msgs;\n    _messagesTruncated = false;\n    _oldestIdx = 0;\n    _syncToolCallsForLoadedMessages(msgs, data.session.tool_calls);" in SESSIONS_JS
+
+
+def test_sessions_js_clears_session_tool_calls_when_messages_have_own_metadata():
+    assert "const hasTc=Array.isArray(m.tool_calls)&&m.tool_calls.length>0;" in SESSIONS_JS
+    assert "const hasTu=Array.isArray(m.content)&&m.content.some(p=>p&&p.type==='tool_use');" in SESSIONS_JS
+    assert "windowOffset" not in SESSIONS_JS
+    assert "copy.assistant_msg_idx=idx-offset;" not in SESSIONS_JS
+    assert "S.toolCalls=sessionToolCalls.map(tc=>({...tc,done:true}));" in SESSIONS_JS
+    assert "S.toolCalls=[];" in SESSIONS_JS