diff --git a/ui/src/styles/chat/layout.css b/ui/src/styles/chat/layout.css
index 8c68a2327b4..c9a9b43735a 100644
--- a/ui/src/styles/chat/layout.css
+++ b/ui/src/styles/chat/layout.css
@@ -363,8 +363,10 @@
   box-sizing: border-box;
 }
 
+/* Fix #45707: Ensure input always accessible, even when empty state renders */
 .agent-chat__input {
   position: relative;
+  z-index: 100; /* Force above empty state overlay */
   display: flex;
   flex-direction: column;
   margin: 0 18px 14px;
@@ -903,6 +905,7 @@
 }
 
 /* Welcome state (new session) */
+/* Fix #45707: Constrain to message area, never cover input */
 .agent-chat__welcome {
   display: flex;
   flex-direction: column;
@@ -913,6 +916,14 @@
   padding: 48px 24px;
   flex: 1;
   min-height: 0;
+  /* Ensure welcome state stays below input box in stacking context */
+  z-index: 1;
+  pointer-events: none; /* Allow clicks to pass through to input area */
+}
+
+/* Re-enable pointer events on interactive elements within welcome state */
+.agent-chat__welcome > * {
+  pointer-events: auto;
 }
 
 .agent-chat__welcome-glow {
diff --git a/ui/src/styles/chat/sidebar.css b/ui/src/styles/chat/sidebar.css
index de6010f3ed7..9e1d4483da6 100644
--- a/ui/src/styles/chat/sidebar.css
+++ b/ui/src/styles/chat/sidebar.css
@@ -9,6 +9,7 @@
 
 .chat-main {
   min-width: 400px;
+  min-height: 0; /* Prevent flex overflow that can hide input area */
   display: flex;
   flex-direction: column;
   overflow: hidden;
diff --git a/ui/src/ui/views/chat.empty-state.test.ts b/ui/src/ui/views/chat.empty-state.test.ts
new file mode 100644
index 00000000000..31dba98b538
--- /dev/null
+++ b/ui/src/ui/views/chat.empty-state.test.ts
@@ -0,0 +1,105 @@
+/**
+ * Tests for #45707 - WebChat empty state overlay blocking input
+ *
+ * This test ensures that sessions with tool-call messages (heartbeat/cron),
+ * streaming content, or live streams are not treated as empty, preventing
+ * the welcome overlay from blocking the input box.
+ */
+
+import { describe, it, expect } from "vitest";
+
+describe("chat empty state logic (#45707)", () => {
+  it("should not treat session with tool messages as empty", () => {
+    const messages: unknown[] = [];
+    const toolMessages: unknown[] = [{ role: "tool", content: "Heartbeat", timestamp: Date.now() }];
+    const streamSegments: Array<{ text: string; ts: number }> = [];
+    const stream: string | null = null;
+
+    const hasSessionActivity =
+      messages.length > 0 ||
+      toolMessages.length > 0 ||
+      streamSegments.some((segment) => segment.text.trim()) ||
+      stream !== null;
+
+    expect(hasSessionActivity).toBe(true);
+  });
+
+  it("should treat truly empty session as empty", () => {
+    const messages: unknown[] = [];
+    const toolMessages: unknown[] = [];
+    const streamSegments: Array<{ text: string; ts: number }> = [];
+    const stream: string | null = null;
+
+    const hasSessionActivity =
+      messages.length > 0 ||
+      toolMessages.length > 0 ||
+      streamSegments.some((segment) => segment.text.trim()) ||
+      stream !== null;
+
+    expect(hasSessionActivity).toBe(false);
+  });
+
+  it("should not treat session with history messages as empty", () => {
+    const messages: unknown[] = [{ role: "user", content: "Hello", timestamp: Date.now() }];
+    const toolMessages: unknown[] = [];
+    const streamSegments: Array<{ text: string; ts: number }> = [];
+    const stream: string | null = null;
+
+    const hasSessionActivity =
+      messages.length > 0 ||
+      toolMessages.length > 0 ||
+      streamSegments.some((segment) => segment.text.trim()) ||
+      stream !== null;
+
+    expect(hasSessionActivity).toBe(true);
+  });
+
+  it("should not treat session with streaming content as empty", () => {
+    const messages: unknown[] = [];
+    const toolMessages: unknown[] = [];
+    const streamSegments: Array<{ text: string; ts: number }> = [
+      { text: "Streaming response...", ts: Date.now() },
+    ];
+    const stream: string | null = null;
+
+    const hasSessionActivity =
+      messages.length > 0 ||
+      toolMessages.length > 0 ||
+      streamSegments.some((segment) => segment.text.trim()) ||
+      stream !== null;
+
+    expect(hasSessionActivity).toBe(true);
+  });
+
+  it("should not treat session with live stream as empty", () => {
+    const messages: unknown[] = [];
+    const toolMessages: unknown[] = [];
+    const streamSegments: Array<{ text: string; ts: number }> = [];
+    const stream: string | null = "Live streaming...";
+
+    const hasSessionActivity =
+      messages.length > 0 ||
+      toolMessages.length > 0 ||
+      streamSegments.some((segment) => segment.text.trim()) ||
+      stream !== null;
+
+    expect(hasSessionActivity).toBe(true);
+  });
+
+  it("should handle mixed messages and streaming", () => {
+    const messages: unknown[] = [{ role: "user", content: "Check", timestamp: Date.now() }];
+    const toolMessages: unknown[] = [{ role: "tool", content: "Cron", timestamp: Date.now() }];
+    const streamSegments: Array<{ text: string; ts: number }> = [
+      { text: "Thinking...", ts: Date.now() },
+    ];
+    const stream: string | null = null;
+
+    const hasSessionActivity =
+      messages.length > 0 ||
+      toolMessages.length > 0 ||
+      streamSegments.some((segment) => segment.text.trim()) ||
+      stream !== null;
+
+    expect(hasSessionActivity).toBe(true);
+  });
+});
diff --git a/ui/src/ui/views/chat.ts b/ui/src/ui/views/chat.ts
index 88a712706f0..9797ed55d44 100644
--- a/ui/src/ui/views/chat.ts
+++ b/ui/src/ui/views/chat.ts
@@ -850,7 +850,16 @@ export function renderChat(props: ChatProps) {
   };
 
   const chatItems = buildChatItems(props);
-  const isEmpty = chatItems.length === 0 && !props.loading;
+  // Fix #45707: Check for any session activity, not just renderable messages
+  // Includes tool-call messages (heartbeat/cron), streaming content, and live streams
+  const hasSessionActivity =
+    (Array.isArray(props.messages) && props.messages.length > 0) ||
+    (Array.isArray(props.toolMessages) && props.toolMessages.length > 0) ||
+    (Array.isArray(props.streamSegments) &&
+      props.streamSegments.some((segment) => segment.text.trim())) ||
+    props.stream !== null;
+  const showWelcomeState = !hasSessionActivity && !props.loading && !vs.searchOpen;
+  const showEmptySearch = chatItems.length === 0 && !props.loading && vs.searchOpen;
 
   const thread = html`
     <div
@@ -893,9 +902,9 @@ export function renderChat(props: ChatProps) {
             `
           : nothing
       }
-      ${isEmpty && !vs.searchOpen ? renderWelcomeState(props) : nothing}
+      ${showWelcomeState ? renderWelcomeState(props) : nothing}
       ${
-        isEmpty && vs.searchOpen
+        showEmptySearch
           ? html`
               <div class="agent-chat__empty">No matching messages</div>
             `