Walker came back to the US later that year, signing with the MetroStars, after starting goalkeeper Tim Howard signed with Manchester United. In 2003 with the MetroStars, Walker became the third goalkeeper in MLS history to finish a season with sub-1.00 Goals Against Average (GAA), capturing the league-best 0.95 GAA. 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. In 2005, The MetroStars signed Tony Meola and traded Walker to the Columbus Crew. 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. At the end of 2005 season, Walker injured his back and was sidelined until he retired in 2006 due to a chronic, inoperable back injury.