diff --git a/scripts/hooks/cost-tracker.js b/scripts/hooks/cost-tracker.js
index 8eb605274..3de1eaaec 100755
--- a/scripts/hooks/cost-tracker.js
+++ b/scripts/hooks/cost-tracker.js
@@ -92,6 +92,13 @@ function toNumber(v) {
  * Scan the session JSONL and sum token usage across all assistant turns.
  * Returns { inputTokens, outputTokens, cacheWriteTokens, cacheReadTokens, model }
  * or null on read failure.
+ *
+ * Claude Code writes one JSONL line per content block, so a single API
+ * response (one message.id) spans multiple assistant lines that each repeat
+ * the same message.usage. Summing every line inflates totals ~2.5-3x
+ * (verified: a session with 704 assistant lines had only 286 unique
+ * message.ids — $867 line-summed vs $333 deduped). Usage is therefore
+ * counted once per message.id, keeping the last line seen for each id.
  */
 function sumUsageFromTranscript(transcriptPath) {
   let content;
@@ -101,10 +108,8 @@ function sumUsageFromTranscript(transcriptPath) {
     return null;
   }
 
-  let inputTokens = 0;
-  let outputTokens = 0;
-  let cacheWriteTokens = 0;
-  let cacheReadTokens = 0;
+  const usageById = new Map();
+  let syntheticKey = 0;
   let model = 'unknown';
 
   for (const line of content.split('\n')) {
@@ -116,13 +121,26 @@ function sumUsageFromTranscript(transcriptPath) {
     const msg = entry.message;
     if (!msg || !msg.usage) continue;
 
-    const u = msg.usage;
+    // Lines without a message.id (older transcript shapes) keep the previous
+    // per-line behavior via a synthetic key.
+    const key = (typeof msg.id === 'string' && msg.id)
+      ? msg.id
+      : `__line_${++syntheticKey}`;
+    usageById.set(key, msg.usage);
+
+    if (msg.model && msg.model !== 'unknown') model = msg.model;
+  }
+
+  let inputTokens = 0;
+  let outputTokens = 0;
+  let cacheWriteTokens = 0;
+  let cacheReadTokens = 0;
+
+  for (const u of usageById.values()) {
     inputTokens      += toNumber(u.input_tokens);
     outputTokens     += toNumber(u.output_tokens);
     cacheWriteTokens += toNumber(u.cache_creation_input_tokens);
     cacheReadTokens  += toNumber(u.cache_read_input_tokens);
-
-    if (msg.model && msg.model !== 'unknown') model = msg.model;
   }
 
   return { inputTokens, outputTokens, cacheWriteTokens, cacheReadTokens, model };
diff --git a/tests/hooks/cost-tracker.test.js b/tests/hooks/cost-tracker.test.js
index 117e4db23..8f652d7a1 100644
--- a/tests/hooks/cost-tracker.test.js
+++ b/tests/hooks/cost-tracker.test.js
@@ -129,6 +129,42 @@ function runTests() {
     fs.rmSync(tmpHome, { recursive: true, force: true });
   }) ? passed++ : failed++);
 
+  // 2b. Dedupes usage by message.id (one API response = many JSONL lines)
+  (test('counts usage once per message.id across multi-line responses', () => {
+    const tmpHome = makeTempDir();
+    const transcriptPath = path.join(tmpHome, 'session.jsonl');
+    const sharedUsage = {
+      input_tokens: 1000,
+      output_tokens: 500,
+      cache_creation_input_tokens: 200,
+      cache_read_input_tokens: 300,
+    };
+    writeTranscript(transcriptPath, [
+      // One API response split into 3 content-block lines, all carrying the
+      // same message.id and the same usage — must be counted exactly once.
+      { type: 'assistant', message: { id: 'msg_01AAA', model: 'claude-sonnet-4-20250514', usage: sharedUsage } },
+      { type: 'assistant', message: { id: 'msg_01AAA', model: 'claude-sonnet-4-20250514', usage: sharedUsage } },
+      { type: 'assistant', message: { id: 'msg_01AAA', model: 'claude-sonnet-4-20250514', usage: sharedUsage } },
+      // A second, distinct response.
+      { type: 'assistant', message: { id: 'msg_01BBB', model: 'claude-sonnet-4-20250514', usage: { input_tokens: 25, output_tokens: 5 } } },
+    ]);
+
+    const result = runScript(
+      { session_id: 'dedupe-session', transcript_path: transcriptPath },
+      withTempHome(tmpHome)
+    );
+    assert.strictEqual(result.code, 0, `Expected exit code 0, got ${result.code}`);
+
+    const metricsFile = path.join(tmpHome, '.claude', 'metrics', 'costs.jsonl');
+    const row = JSON.parse(fs.readFileSync(metricsFile, 'utf8').trim());
+    assert.strictEqual(row.input_tokens, 1025, 'Expected msg_01AAA usage counted once, not 3x');
+    assert.strictEqual(row.output_tokens, 505, 'Expected msg_01AAA usage counted once, not 3x');
+    assert.strictEqual(row.cache_write_tokens, 200, 'Expected cache write counted once per message.id');
+    assert.strictEqual(row.cache_read_tokens, 300, 'Expected cache read counted once per message.id');
+
+    fs.rmSync(tmpHome, { recursive: true, force: true });
+  }) ? passed++ : failed++);
+
   // 3. Handles empty input gracefully
   (test('handles empty input gracefully', () => {
     const tmpHome = makeTempDir();