After signing with the New York Yankees, Koy's contract was sold to the Brooklyn Dodgers on April 15, 1938.

Koy finished the year ranking second in the NL with 15 stolen bases, and ninth with a .468 slugging average.

He was traded on June 12, 1940 to the St. Louis Cardinals with Bert Haas, Sam Nahem and Carl Doyle and $125,000 for Curt "Coonskin" Davis and Joe "Ducky" Medwick.

Koy appeared in 78 games with the Phillies, and was eventually released from his contract May 27, 1946 after serving in the Navy during World War II.

His son Ernie Koy, Jr. starred on the 1963 National Champion Texas Longhorn football team.