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After graduating Norwalk High School in Norwalk, Iowa, he turned down a scholarship to play baseball at the University of Nebraska and entered the June 2000 Major League Baseball Draft. At that time, he was ranked as the 70th-best prospect in the nation by Baseball America. He was drafted and signed by the Los Angeles Dodgers.
In his first full season with Dodgers Triple-A affiliate, the Las Vegas 51s, Hanrahan went 7-7 with an Earned Run Average of 5.05 in 25 games. He ranked second on the club with 22 starts and third with 119.1 innings pitched. He batted .281 on the season and hit a home run on May 4 against Tucson and posted a 4.11 ERA at home and 6.39 mark on the road in the Pacific Coast League.
Afer the season, Hanrahan opted for minor league free agency, and five days later, on November 6, 2006 the Washington Nationals signed him to a one-year contract. He didn't make the team out of spring training, and so started with AAA-Columbus, starting 17 games, going 5-4 with a 3.70 ERA. The Nationals, their starting pitching decimated by injuries, purchased Hanrahan's contract in late July, and on July 28, 2007, Hanrahan made his major league debut against the New York Mets. In that game, he gave up three runs in six innings, striking out seven, and hitting a triple in his first at-bat. He did not receive a decision, but the Nationals defeated the Mets 6-5. One week later on August 4, 2007, Hanrahan got his first big league victory over the St. Louis Cardinals, allowing 1 run and 6 hits in 5 2/3 innings, and helping his cause by hitting a 2-run double.
On June 30, 2009 the Nationals traded Hanrahan and Lastings Milledge to the Pittsburgh Pirates for Nyjer Morgan and Sean Burnett. Hanrahan has made two All-Star games with the Pirates in 2011 and 2012.
Hanrahan officially announced his retirement from baseball on November 15, 2016.