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 managed in minor leagues for six seasons. He led the unaffiliated Houston Buffs of the American Association from part of 1959 to most of 1964. Following this, he coached pitchers for the Washington Senators, New York Mets, and Atlanta Braves, working with managers such as Gil Hodges, Yogi Berra, and Joe Torre.