Hottovy began his professional career as a starting pitcher with the Lowell Spinners in 2004. In innings with Lowell, the left hander gave up three earned runs. The following season he was promoted to High-A Wilmington, where he had a 5.45 ERA and a 3–12 record in 23 starts. He split the 2006 season between Wilmington and the Portland Sea Dogs, with a 10–10 record and a 3.15 ERA between the two teams. He spent 2007 and 2008 with Portland, recording 5.61 and 5.00 ERAs in those seasons, respectively. In 2009, he became a full-time relief pitcher. He was sent back to Low-A Lowell for five games before returning to Portland. As a reliever from 2009 to 2011 with Lowell, Portland, and the Triple-A Pawtucket Red Sox, he appeared in 76 games, giving up 63 runs in innings. Hottovy was called up to the major leagues for the first time on June 3, 2011. He got the Red Sox out of jams in his first two MLB outings, inducing a ground-out and a double play, both to end innings. In total, he made eight appearances for Boston, allowing three earned runs in four innings of work before being designated for assignment on July 16. He was then sent outright to Pawtucket on July 20. In September, Hottovy was named the inaugural recipient of the Red Sox' Lou Gorman Award.
Kansas City Royals
Hottovy became a free agent on November 2, 2011, and signed with the Kansas City Royals on November 15. Hottovy split his time between the Royals and Triple-A Omaha. In 9 games with the Royals, Hottovy had a 2.89 ERA with 6 strikeouts in innings. With Omaha, he had 7 saves in 41 games and a 2.52 ERA while striking out 61 in 50 innings. On November 2, 2012, the Royals designated Hottovy for assignment.
Late career
;Texas Rangers On November 8, 2012, Hottovy was acquired by the Texas Rangers for a player to be named later or cash considerations. On January 7, 2013, Hottovy was designated for assignment to make room for Lance Berkman on the roster. ;Toronto Blue Jays Hottovy was claimed off waivers by the Toronto Blue Jays on January 10, 2013. The Blue Jays designated Hottovy for assignment on January 11, 2013, to make room for Henry Blanco on their roster. Hottovy was outrighted to the Buffalo Bisons on January 16. Hottovy started the 2013 season with the Double-A New Hampshire Fisher Cats, and was promoted to the Buffalo Bisons on June 4. He became a free agent on October 1. ;Chicago Cubs The Chicago Cubs signed Hottovy to a minor league contract with an invitation to major league spring training on December 12, 2013. He was released on April 27, 2014.
Post-playing career
Hottovy was hired by the Chicago Cubs to serve as the team's Run Prevention Coordinator in December 2014. He served in that position until he was named the Cubs' pitching coach on December 6, 2018. He remained pitching coach after the Cubs chose not to have Joe Maddon return and after the hiring of David Ross as Cubs' manager in 2019. Hottovy contracted the COVID-19 virus during the 2020 pandemic, but had recovered by the time teams returned to summer camp prior to the start of the 2020 season.
