McKernan received the John P. McPhail Trophy for best minor league executive twice, making him the only two-time winner. He also won The Sporting News Minor League Executive of the Year Award on two occasions and was a three-time recipient of the Pacific Coast League Executive of the Year Award (1981, 1982, and 1991). In 2000, he was named the King of Baseball at the annual Minor League Baseball winter meetings. He is a member of the New Mexico Sports Hall of Fame in Albuquerque, the Albuquerque Baseball Hall of Fame, and the Unico of Pittsfield Berkshire County Baseball Hall of Fame.