In the 2000 MLB draft, Hanrahan was selected in the second round (No. 57 overall) and signed by the Los Angeles Dodgers. In 2000, Hanrahan played for the Great Falls Dodgers and in 2001, for the Wilmington Waves. Hanrahan split the 2002 season between the Vero Beach Dodgers and the Jacksonville Suns. In 2003, he played for Jacksonville and the Dodgers Triple-A affiliate, the Las Vegas 51s. In 2004, his first full season with Las Vegas, Hanrahan went 7–7 with an earned run average (ERA) of 5.05 in 25 games, ranked second on the club with 22 starts, ranked third with 119 innings pitched, batted .281 on the season and hit a home run on May 4 against the Tucson Sidewinders and posted a 4.11 ERA at home and 6.39 mark on the road in the Pacific Coast League. After the 2006 season, Hanrahan became a free agent.
