After graduating from Andover High School in 1999, Hanigan attended Rollins College, where he signed as an undrafted free agent with the Cincinnati Reds.

He then spent the 2002 to 2006 seasons with Reds minor league baseball teams, including the Dayton Dragons and Louisville Bats.

[2] At Andover High School, Hanigan was a three-year varsity starter, and was named an Eagle-Tribune and Eastern Massachusetts All-Star during his senior season, in which he hit .397.

[5] He attended Rollins College in Winter Park, Florida, where he played third base or left field because of an upperclassman at the catcher position.

[7] In his junior year, he hit .384 with 48 RBIs over 57 games for Rollins,[1] as the team finished 41–16 and clinched a berth to the NCAA Division II Baseball Championship.

[14] Hanigan was named to the East squad in the Midwest League All-Star Game, where he served as the reserve catcher.

[13] Hanigan spent the entire 2004 season with the Class A-Advanced Potomac Cannons, where he served as the team's catcher and designated hitter.

[18] For the season, Hanigan hit .296 with five home runs and 56 RBIs over 119 games as the Cannons made the Carolina League Northern Division playoffs for the first time since 1995.

During a July 13, 2006 contest, Hanigan drove in what would be the winning run with two outs in the seventh inning against the Birmingham Barons.

[29] Hanigan went on the DL after he was hit on the face mask by a foul tip and suffered a concussion; he returned on August 8, 2009.

[32] Against Chicago Cubs pitcher Sean Marshall, Hanigan drove in the tie-breaking run in what was an 8–7 win for the Reds on August 7.

[7][34] Hanigan caught both of Homer Bailey's no-hitters, against the Pittsburgh Pirates on September 28, 2012, and against the San Francisco Giants on July 2, 2013.

On June 17 he had a home run and a walk against the Baltimore Orioles, but he then missed several more games due to neck stiffness and later with soreness in his left side.

[39] On April 17, 2015, Hanigan hit his first home run in a Red Sox uniform off of Ubaldo Jiménez of the Baltimore Orioles.

[42] Hanigan finished the 2016 season with a .171 batting average, and despite playing in only 34 games he led the major leagues in passed balls, with 18.

[43] On November 2, 2016, the Red Sox declined to pick up Hanigans team option, thus making him a free agent.

After being released by the Phillies, Hanigan agreed to a minor league contract with the Colorado Rockies, on March 28, 2017.

In March 2024, the Williamsport Crosscutters hired Hanigan to be their manager during the 2024 MLB Draft League Season.