A very good hitting catcher, Murphy was drafted by the Houston Astros in 1986. After one season with the Astros, John moved to the St. Louis Cardinals farm system, where he remained for several seasons.

He was a central figure as a catcher for the St. Louis Union Printers, who won back-to-back national championships in 1984 and 1985. In 2002, Murphy was inducted into the Union Printers International Baseball League Hall of Fame. He played one season for the Royals in the Metro Collegiate League and has worked at Jim Dix baseball camps.