In , Merrill began the season with Columbus before getting the call to take charge of the New York Yankees in June when Bucky Dent was fired as manager. Merrill finished out what would be one of the worst seasons in Yankees history. The Yankees finished 67-95 (49-64 under Merrill), dead last in the American League and second-worst in baseball. It was only the fourth time that the storied franchise had finished with the worst record in the league. However, Merrill was not blamed for the debacle and was brought back for the season—the first time in four years that the Yankees had a single manager for the entire season. However, after the Yankees could only improve to 71-91, he was replaced by Buck Showalter prior to the 1992 season and served that season as a roving minor-league instructor.