He has also played in Nippon Professional Baseball (NPB) for the Chiba Lotte Marines being one of the most highly known pitchers in Japan during the 2010 season.

After attending California State University, Northridge for three years, Murphy was selected as the 98th overall pick in the third-round of the 2002 famous Moneyball draft.

He spent two seasons in the Athletics organization, pitching for the Vancouver Canadians (2002), Kane County Cougars (2003) and Midland RockHounds (2003).

On July 30, 2004, Murphy was traded along with Hee-Seop Choi and Brad Penny to the Los Angeles Dodgers for Paul Lo Duca, Juan Encarnación, and Guillermo Mota.

The next day, on July 31, 2004, he was traded once again, this time to the Arizona Diamondbacks along with Koyie Hill and Reggie Abercrombie for Steve Finley and Brent Mayne.

Murphy spent the whole 2005 season with the Triple-A Tucson Sidewinders but performed poorly as he had a 5.65 ERA in 23 games (21 starts).

He made his Major League debut against the San Diego Padres on September 3, working 1.2 innings in relief and allowing three earned runs on 3 hits and 3 walks.

In 2010 Murphy led the Chiba Lotte Marines to the Japan World Series helping the team to win the championship along with being one of the top pitchers starting off the year undefeated 6-0 until his first loss against Yu Darvish.

He returned to the Blue Jays on a minor league contract on January 17, 2012, and was assigned to the Triple-A Las Vegas 51s.

Murphy played the 2013 season for the Long Island Ducks of the Atlantic League of Professional Baseball, helping lead them to yet another championship.