diff --git a/.changeset/eighty-dots-train.md b/.changeset/eighty-dots-train.md
new file mode 100644
index 000000000..169bdc7cb
--- /dev/null
+++ b/.changeset/eighty-dots-train.md
@@ -0,0 +1,5 @@
+---
+'myst-cli': patch
+---
+
+effectively discard files matched by pattern if already mentioned
diff --git a/packages/myst-cli/src/project/fromTOC.ts b/packages/myst-cli/src/project/fromTOC.ts
index 6ad01d00d..dd5bfb75c 100644
--- a/packages/myst-cli/src/project/fromTOC.ts
+++ b/packages/myst-cli/src/project/fromTOC.ts
@@ -120,7 +120,8 @@ export function patternsToFileEntries(
         const { pattern, sort, ...leftover } = entry as PatternEntry;
         // Glob matches, relative to `path`, ordered naturally
         let matches = globSync(pattern, { cwd: path, nodir: true, ...opts })
-          .filter((item) => !ignore || !ignore.includes(item))
+          // ignore contains resolved entries, so we need to search for item resolved
+          .filter((item) => !ignore || !ignore.includes(resolve(path, item)))
           .sort(comparePaths);
         // Reverse order if descending sort is requested
         if (sort === 'descending') {
diff --git a/packages/myst-cli/src/project/toc.pattern.spec.ts b/packages/myst-cli/src/project/toc.pattern.spec.ts
index 6d6c7cd14..ecc5b25e6 100644
--- a/packages/myst-cli/src/project/toc.pattern.spec.ts
+++ b/packages/myst-cli/src/project/toc.pattern.spec.ts
@@ -1,4 +1,5 @@
 import { describe, expect, it, beforeEach, vi } from 'vitest';
+import { resolve } from 'node:path';
 import memfs from 'memfs';
 import { Session } from '../session';
 import { listExplicitFiles, patternsToFileEntries } from './fromTOC';
@@ -141,6 +142,21 @@ describe('patternsToFileEntries', () => {
       { file: 'meetings/2026-01-01.md', implicit: true },
     ]);
   });
+  it('explicitly listed files are excluded from subsequent glob patterns', () => {
+    memfs.vol.fromJSON({
+      'index.md': '',
+      'test1.md': '',
+      'test2.md': '',
+    });
+    // Simulate ignore list built from explicit file entries (absolute paths, as listExplicitFiles returns)
+    const cwd = '.';
+    const ignore = [resolve(cwd, 'index.md'), resolve(cwd, 'test1.md')];
+    expect(
+      patternsToFileEntries(session, [{ pattern: '*.md' }], cwd, ignore, '/tmp/warn.txt', {
+        fs: memfs,
+      }),
+    ).toEqual([{ file: 'test2.md', implicit: true }]);
+  });
 });
 
 describe('listExplicitFiles', () => {