In 1962, Klein was named head coach again, replacing El Tappe and managing 30 games between May 1 and June 3 (posting a 12–18 record). The 1962 Cubs finished 59–103 — their first time ever with a 100-loss season, and still the worst in franchise history. Only the 40–120 New York Mets were worse. In 1965, Klein was named to a third stint as head coach, replacing Bob Kennedy on June 14 and staying on through the rest of the season. The last head coach in the history of the College of Coaches, Klein went 48–58 in 1965, and finished with a lifetime 65–82 (.442) record. He remained in the Cub organization as a scout.