Walker then was a minor league manager for six seasons. He helmed the unaffiliated Houston Buffs of the American Association for part of 1959, then managed at Double-A in the Dodgers' and Yankees' farm systems from 1960 through 1964. After  he was a pitching coach for the Washington Senators, New York Mets and Atlanta Braves, working closely with managers Gil Hodges, Yogi Berra and Joe Torre, among others.
Walker was the Mets' pitching coach for 14 seasons, from 1968 through 1981, including service on the 1969 World Champion "Amazin'" Mets. He also served as the club's emergency manager from September 25–29, , after Hodges suffered a mild heart attack and went on medical leave for the final four games of the season; under Walker, the Mets were 2–2. As the Mets' pitching coach, he supervised Hall of Famers Tom Seaver and Nolan Ryan.