Klinkhammer played his first professional season in 2007–08 with the Norfolk Admirals of the American Hockey League. He made his professional debut on October 19, 2007, against the Binghamton Senators, providing an assist. He then scored his first career professional goal on November 23 against the Springfield Falcons, adding two assists for the Admirals' 4–2 win. On June 8, 2009, Klinkhammer signed as a free agent with the Rockford IceHogs, the AHL affiliate of the NHL's Chicago Blackhawks, to a two-year, entry-level contract. Following an injury to Blackhawks forward Patrick Kane, Klinkhammer was recalled from Rockford to make his NHL debut on December 10, 2010, dressing for a home game win over the Dallas Stars. On July 11, 2011, Klinkhammer signed a one-year contract extension with Chicago. On December 2, 2011, Klinkhammer was traded to the Ottawa Senators in exchange for a conditional seventh-round draft pick in 2013. He reported to the Senators' AHL affiliate, the Binghamton Senators. He played in his second NHL game, and first with the Senators, on March 4, 2012, against the Florida Panthers. After the game, Ottawa Head CoachPaul MacLean was impressed, calling Klinkhammer "one of our best players." On July 3, 2012, Klinkhammer signed as a free agent with the Phoenix Coyotes. With the 2012–13 NHL lockout in effect, however, he was assigned to the team's AHL affiliate, the Portland Pirates. He scored his first career hat-trick October 23, 2012. When the lockout was resolved in January 2013, Klinkhammer remained with Portland, though he was eventually recalled to the Coyotes, later earning the nickname "The Colonel" after his surname's resemblance to the fictional character Colonel Klink's from the TV sitcom Hogan's Heroes. On December 5, 2014, Klinkhammer, along with a conditional fifth-round pick in 2016, was traded to the Pittsburgh Penguins in exchange for defenceman Philip Samuelsson. On January 2, 2015, Klinkhammer and a first-round pick in 2015 were traded to the Edmonton Oilers in exchange for David Perron. On January 6, Klinkhammer landed a blindside-hit on Detroit Red Wings forward Johan Franzén, causing the latter a severe concussion that ended his season. On February 20, Klinkhammer signed a one-year, $650,000 contract extension with the Oilers, keeping him with the organization through to the conclusion of the 2015–16 season. He finished the 2014–15 season with five goals and four assists from 69 games split between the Coyotes, Penguins and Oilers. After 6 seasons in the NHL, Klinkhammer opted to sign as a free agent to a two-year deal with Belarusian club, HC Dinamo Minsk of the KHL on June 17, 2016. In Game 5 of the 2018 Gagarin Cup Final against CSKA Moscow, Klinkhammer scored the game-winning goal for Ak Bars Kazan, allowing them to win the Gagarin Cup for the third time since KHL's inception. On July 25, 2020, Klinkhammer continued his career in the KHL, returning to Belarussian club, Dinamo Minsk, as a free agent on a one-year contract.