Murton was acquired at the 2004 trading deadline by the Chicago Cubs along with Red Sox star shortstop and fellow former Georgia Tech Yellow Jacket Nomar Garciaparra as part of a four-team blockbuster deal.

He started 2005 with the Double-A West Tenn Diamond Jaxx, but was called up to the major leagues for the first time on July 8, along with Adam Greenberg, to replace the struggling Corey Patterson and Jason Dubois.

[7] He continued his success in the majors over the rest of the season, hitting .321 with two stolen bases, seven home runs, and an on-base percentage of .386 in 51 games in 2005.

On June 13, after hitting only one home run with eight RBIs in limited playing time, Murton was optioned to Triple-A to make room for left-handed pitcher Clay Rapada.

On July 8, 2008, Murton was traded along with Cubs prospects Josh Donaldson, Eric Patterson, and Sean Gallagher to the Oakland Athletics for pitchers Rich Harden and Chad Gaudin.

When stepping to the plate at Rockies home games, the song "Strong Tower" by Kutless was played over the speaker system.

On December 4, 2009, Murton was released by the Rockies,[12] who sold his contract to the Hanshin Tigers of Japan's Nippon Professional Baseball.

On February 16, 2016, Murton returned to MLB and signed a minor league contract with the Chicago Cubs organization.