Walker played professionally in Chile and the United States, including two stints with Major League Soccer (MLS).
He then played one season with the University of Louisville and still holds the record for most saves in a match (17), versus Evansville (September 8, 1994).
They loaned him out to Club Deportivo Huachipato of Chile's First Division in 1998, in which we was named Team MVP, then U. Catolica brought him back the following year.
He became the starting goalkeeper for the club, playing in multiple Copa Libertadores tournaments, which included wins against Argentina's Boca Juniors and Brazil's Flamengo.
That same year, Walker was the MLS Player of the Month for August and the MetroStars finished as Runners-Up in the US Open Cup.
With the Crew, Walker won the team's 2005 Defensive Player of the Year and finished second in MLS with a GAA of 1.12.
Walker started and played three matches for the United States Men's National Team, including a 1–0 shutout win over Mexico on April 28, 2004.
In the fall of 2009, Jonny Walker became the Goalkeeper Coach for the University of Memphis Women's Soccer Team.