Lopat managed the Triple-A Richmond Virginians for the Yankees from 1956–58, then became a roving pitching coach in the Bombers' farm system in 1959. In , he served one season the Yankees' MLB pitching coach during Casey Stengel's final campaign as the club's manager. That year produced an American League pennant for the Yankees, but a defeat at the hands of the Pittsburgh Pirates in the World Series. Lopat was not rehired by Stengel's successor, Ralph Houk, but he stayed in the league as pitching coach of the Minnesota Twins in and the Kansas City Athletics in .