diff --git a/src/panels/MainPanel.ts b/src/panels/MainPanel.ts
index 5869905d..d653856e 100644
--- a/src/panels/MainPanel.ts
+++ b/src/panels/MainPanel.ts
@@ -365,6 +365,14 @@ export class MainPanel {
     if (samePath(newPath, this.repoPath)) { return; }
     this.swapRepo(newPath);
 
+    // The discovered list can lag behind the repo VS Code's SCM switched to
+    // (e.g. it sits deeper than discovery scans). Add the active repo so the
+    // webview can resolve its header/dropdown entry instead of falling back to
+    // the first repo while the graph already shows the new one. See issue #96.
+    if (!this.cachedRepos.some(r => samePath(r.path, this.repoPath))) {
+      this.cachedRepos = [...this.cachedRepos, { path: this.repoPath, name: path.basename(this.repoPath), type: 'root' }];
+    }
+
     this.post({
       type: 'repoList',
       payload: { repos: this.cachedRepos, active: this.repoPath },
diff --git a/src/panels/__tests__/MainPanel.test.ts b/src/panels/__tests__/MainPanel.test.ts
index 76051ee3..f16e5c41 100644
--- a/src/panels/__tests__/MainPanel.test.ts
+++ b/src/panels/__tests__/MainPanel.test.ts
@@ -287,6 +287,19 @@ describe('MainPanel message routing', () => {
     await dispatch({ type: 'switchRepo', payload: { path: '/somewhere/else' } });
     expect(postedOfType('error').length).toBeGreaterThan(0);
   });
+
+  it('posts a repoList that includes the active repo when SCM switches to one discovery missed (issue #96)', async () => {
+    await new Promise(r => setTimeout(r, 0)); // let sendRepoList populate cachedRepos
+    // The extension-driven switch (VS Code SCM focus change) bypasses the
+    // webview allow-list, so the target can be absent from the discovered list.
+    await MainPanel.currentPanel!.switchRepo('/deep/repo-b');
+
+    const list = postedOfType('repoList').at(-1)!;
+    const repos = list.payload!.repos as Array<{ path: string; name: string }>;
+    expect(list.payload!.active).toBe('/deep/repo-b');
+    expect(repos.some(r => r.path === '/deep/repo-b')).toBe(true);
+    expect(repos.find(r => r.path === '/deep/repo-b')!.name).toBe('repo-b');
+  });
 });
 
 describe('MainPanel error handling', () => {
diff --git a/webview-ui/src/__tests__/App.test.ts b/webview-ui/src/__tests__/App.test.ts
index 69b013b7..52902df6 100644
--- a/webview-ui/src/__tests__/App.test.ts
+++ b/webview-ui/src/__tests__/App.test.ts
@@ -115,6 +115,28 @@ describe('App — message handling', () => {
     });
   });
 
+  it('repoList keeps the header on the active repo when the list is stale (issue #96)', async () => {
+    // Reproduce the SCM repo-switch path: the extension posts repoList with the
+    // new active path while the discovered list still only holds the old repo.
+    const { container } = render(App);
+    postMsg('repoList', {
+      repos: [{ path: 'C:\\repo\\alpha', name: 'alpha', type: 'root' }],
+      active: 'C:\\repo\\alpha',
+    });
+    await waitFor(() => {
+      expect(container.querySelector('.repo-name')?.textContent?.trim()).toBe('alpha');
+    });
+
+    postMsg('repoList', {
+      repos: [{ path: 'C:\\repo\\alpha', name: 'alpha', type: 'root' }],
+      active: 'C:\\repo\\beta',
+    });
+    await waitFor(() => {
+      expect(uiStore.activeRepo).toBe('C:\\repo\\beta');
+      expect(container.querySelector('.repo-name')?.textContent?.trim()).toBe('beta');
+    });
+  });
+
   it('notGitRepo flips commitStore.notGitRepo', async () => {
     render(App);
     postMsg('notGitRepo');
diff --git a/webview-ui/src/components/layout/Toolbar.svelte b/webview-ui/src/components/layout/Toolbar.svelte
index 6ceb0910..0e58849f 100644
--- a/webview-ui/src/components/layout/Toolbar.svelte
+++ b/webview-ui/src/components/layout/Toolbar.svelte
@@ -9,7 +9,7 @@
   import { tooltip } from '../../lib/actions/tooltip';
   import { modalStore } from '../../lib/stores/modals.svelte';
   import { commitStore } from '../../lib/stores/commits.svelte';
-  import { samePath } from '../../lib/utils/path';
+  import { samePath, repoNameFromPath } from '../../lib/utils/path';
   import type { FlowStatus, FlowBranches } from '../../lib/types';
 
   const vscode = getVsCodeApi();
@@ -96,7 +96,17 @@
   const hasUpstream = $derived(!!branchStore.currentBranch?.upstream && !branchStore.currentBranch?.upstreamGone);
   let ahead = $derived(branchStore.currentBranch?.ahead ?? 0);
   let behind = $derived(branchStore.currentBranch?.behind ?? 0);
-  let activeRepoInfo = $derived(uiStore.repos.find(r => samePath(r.path, uiStore.activeRepo)) ?? uiStore.repos[0]);
+  // The repo list can lag behind the active repo — e.g. VS Code's SCM switches
+  // focus to a repo the extension's discovery did not surface. Resolve the
+  // active path directly in that case: falling back to `repos[0]` would keep
+  // showing the previously active (main) repo while the graph already switched.
+  // See issue #96.
+  let activeRepoInfo = $derived(
+    uiStore.repos.find(r => samePath(r.path, uiStore.activeRepo))
+      ?? (uiStore.activeRepo
+        ? { path: uiStore.activeRepo, name: repoNameFromPath(uiStore.activeRepo), type: 'root' as const }
+        : uiStore.repos[0]),
+  );
 
   const currentBranchName = $derived(branchStore.currentBranch?.name ?? null);
   // git reports non-branch HEAD states as parenthesized pseudo-labels
diff --git a/webview-ui/src/components/layout/__tests__/Toolbar.test.ts b/webview-ui/src/components/layout/__tests__/Toolbar.test.ts
index 8151e1ef..a73d2a6e 100644
--- a/webview-ui/src/components/layout/__tests__/Toolbar.test.ts
+++ b/webview-ui/src/components/layout/__tests__/Toolbar.test.ts
@@ -236,6 +236,23 @@ describe('Toolbar — repo dropdown', () => {
     expect(container.querySelector('.repo-name')?.textContent?.trim()).toBe('main-repo');
   });
 
+  it('shows the active repo even when it is missing from the repo list (issue #96)', () => {
+    // VS Code's SCM can switch to a repo the extension's discovery missed, so
+    // the active path has no entry in the list. The header must follow the
+    // active repo instead of falling back to the first (previously active) one.
+    uiStore.repos = [{ path: 'C:\\repo\\alpha', name: 'alpha', type: 'root' }];
+    uiStore.activeRepo = 'C:\\repo\\beta';
+    const { container } = render(Toolbar);
+    expect(container.querySelector('.repo-name')?.textContent?.trim()).toBe('beta');
+  });
+
+  it('falls back to the first repo before an active repo is known', () => {
+    uiStore.repos = [{ path: '/repo/main', name: 'main-repo', type: 'root' }];
+    uiStore.activeRepo = '';
+    const { container } = render(Toolbar);
+    expect(container.querySelector('.repo-name')?.textContent?.trim()).toBe('main-repo');
+  });
+
   it('chevron and dropdown appear only with multiple repos', async () => {
     uiStore.repos = [
       { path: '/r/a', name: 'a', type: 'root' },
diff --git a/webview-ui/src/lib/utils/__tests__/path.test.ts b/webview-ui/src/lib/utils/__tests__/path.test.ts
index c1edf766..562c3ba1 100644
--- a/webview-ui/src/lib/utils/__tests__/path.test.ts
+++ b/webview-ui/src/lib/utils/__tests__/path.test.ts
@@ -1,5 +1,5 @@
 import { describe, it, expect } from 'vitest';
-import { samePath } from '../path';
+import { samePath, repoNameFromPath } from '../path';
 
 describe('samePath', () => {
   it('matches identical paths', () => {
@@ -28,3 +28,26 @@ describe('samePath', () => {
     expect(samePath('/Users/me/proj', '')).toBe(false);
   });
 });
+
+describe('repoNameFromPath', () => {
+  it('returns the last segment of a POSIX path', () => {
+    expect(repoNameFromPath('/Users/me/projB')).toBe('projB');
+  });
+
+  it('returns the last segment of a Windows path', () => {
+    expect(repoNameFromPath('C:\\Users\\me\\projB')).toBe('projB');
+  });
+
+  it('ignores trailing separators', () => {
+    expect(repoNameFromPath('C:\\Users\\me\\projB\\')).toBe('projB');
+    expect(repoNameFromPath('/Users/me/projB/')).toBe('projB');
+  });
+
+  it('returns the input when there is no separator', () => {
+    expect(repoNameFromPath('projB')).toBe('projB');
+  });
+
+  it('returns an empty string for an empty path', () => {
+    expect(repoNameFromPath('')).toBe('');
+  });
+});
diff --git a/webview-ui/src/lib/utils/path.ts b/webview-ui/src/lib/utils/path.ts
index 62d25f9b..5c4305be 100644
--- a/webview-ui/src/lib/utils/path.ts
+++ b/webview-ui/src/lib/utils/path.ts
@@ -15,3 +15,16 @@ export function samePath(a: string, b: string): boolean {
   if (!a || !b) { return false; }
   return normalize(a) === normalize(b);
 }
+
+/**
+ * Last segment of a filesystem path, used to label a repository whose entry is
+ * missing from the discovered repo list (e.g. VS Code's SCM switched focus to a
+ * repo the filesystem scan did not surface). Handles both separators so Windows
+ * backslash paths work. See issue #96.
+ */
+export function repoNameFromPath(p: string): string {
+  if (!p) { return ''; }
+  const trimmed = p.replace(/[\\/]+$/, '');
+  const idx = Math.max(trimmed.lastIndexOf('/'), trimmed.lastIndexOf('\\'));
+  return idx >= 0 ? trimmed.slice(idx + 1) : trimmed;
+}