diff --git a/sdk/src/query/validate.test.ts b/sdk/src/query/validate.test.ts
index 4f370f541..aa9844db3 100644
--- a/sdk/src/query/validate.test.ts
+++ b/sdk/src/query/validate.test.ts
@@ -643,6 +643,30 @@ describe('validateHealth', () => {
     expect(w006s.some(w => String(w.message).includes('Phase 7'))).toBe(false);
   });
 
+  it('does not emit W006 for unchecked future phases with no directory (#3559)', async () => {
+    await createHealthyPlanning();
+    await writeFile(join(tmpDir, '.planning', 'ROADMAP.md'), [
+      '# Roadmap',
+      '',
+      '## v1.1: Current',
+      '',
+      '- [x] **Phase 21: Active**',
+      '- [ ] **Phase 22: Future planned**',
+      '',
+      '### Phase 21: Active',
+      '',
+      '### Phase 22: Future planned',
+      '',
+    ].join('\n'));
+    await mkdir(join(tmpDir, '.planning', 'phases', '21-active'), { recursive: true });
+
+    const result = await validateHealth([], tmpDir);
+    const data = result.data as Record<string, unknown>;
+    const warnings = data.warnings as Array<Record<string, unknown>>;
+    const w006s = warnings.filter(w => w.code === 'W006');
+    expect(w006s.some(w => String(w.message).includes('Phase 22'))).toBe(false);
+  });
+
   it('does not emit I001 when plan file has descriptor but summary uses canonical stem (#3473)', async () => {
     await createHealthyPlanning();
     await mkdir(join(tmpDir, '.planning', 'phases', '68-bug-surface'), { recursive: true });
diff --git a/sdk/src/query/validate.ts b/sdk/src/query/validate.ts
index e68e072a8..c958c2816 100644
--- a/sdk/src/query/validate.ts
+++ b/sdk/src/query/validate.ts
@@ -598,6 +598,13 @@ export const validateHealth: QueryHandler = async (args, projectDir, workstream)
       while ((m = phasePattern.exec(roadmapContent)) !== null) {
         roadmapPhases.add(m[1]);
       }
+      const notStartedPhases = new Set<string>();
+      const uncheckedPattern = /-\s*\[\s\]\s*\*{0,2}Phase\s+(\d+[A-Z]?(?:\.\d+)*)[:\s*]/gi;
+      let um: RegExpExecArray | null;
+      while ((um = uncheckedPattern.exec(roadmapContent)) !== null) {
+        notStartedPhases.add(um[1]);
+        notStartedPhases.add(String(parseInt(um[1], 10)).padStart(2, '0'));
+      }
 
       const diskPhases = new Set<string>();
       try {
@@ -627,6 +634,7 @@ export const validateHealth: QueryHandler = async (args, projectDir, workstream)
       for (const p of roadmapPhases) {
         const padded = String(parseInt(p, 10)).padStart(2, '0');
         if (!diskPhases.has(p) && !diskPhases.has(padded)) {
+          if (notStartedPhases.has(p) || notStartedPhases.has(padded)) continue;
           addIssue('warning', 'W006', `Phase ${p} in ROADMAP.md but no directory on disk`, 'Create phase directory or remove from roadmap');
         }
       }