Thomas started his junior hockey career with the OHL London Knights in 2008 as the 13th overall selection in the OHL Priority Selection. He was traded to the Generals in the middle of the season in a trade in which London received Michael Del Zotto, John Tavares and Daryl Borden. During the 2008–09 season, Thomas scored four goals each for the Knights and the Generals. In 2009–10, his second OHL season, Thomas scored 41 goals. Tyler Seguin and Jeff Skinner were the only two 2010 first round draft picks to score more goals in junior hockey in 2009–10 than Thomas. He also was credited with 25 assists, for a total of 66 points, leading Oshawa in both goals and points. He had four shorthanded goals during the season, a new Oshawa franchise record. He was named the Eastern Conference's most improved player in a post-season coaches poll, and was also in the top three in several other categories—best shot, hardest shot, most dangerous in goal area, and best stickhandler. In 2010–11, Christian Thomas finished second in the league with 54 goals and sixth in the league in scoring with 99 points, while also tying for the league lead in power play goals. He also finished 5th in the league in game-winning goals with nine. 12 of his regular season goals came against the Kingston Frontenacs, Oshawa's first round playoff opponent. He was named the OHL player of the week three times, including for the first week of the OHL playoffs. At the time Oshawa was eliminated from the OHL playoffs, Thomas was leading the OHL in playoff scoring, and he ended up 7th overall in playoff points and 9th in playoff goals. In the post-season coaches poll, he was named as having the OHL Eastern Conference's best shot and as "most dangerous in the goal area," after finishing as runner up in those categories the prior year. He also repeated his runner-up status as having the conference's hardest shot. Thomas' 95 goals over the 2009–10 and 2010–11 seasons are more than any other OHL player over those two seasons. As a result of Thomas scoring more than 50 goals in 2010–11, Steve and Christian Thomas became the first father son combination to each score 50 goals in a single OHL season. Steve Thomas had scored 51 goals for the Marlboros in 1983–84. Thomas got off to a slow start in the 2011–12 season, marred by a 10-game suspension for a high-sticking incident. However, he recovered and was named the OHL player of the week for the week of November 28 to December 4 for scoring 3 goals and 6 assists with a +6 plus-minus rating in 2 games. He was also named the Canadian Hockey League player of the week for that week, beating out Jérôme Gauthier-Leduc and fellow New York Ranger draftee Michael St. Croix for the honour. He finished the season with 67 points in 55 games with 34 goals and 33 assists. In 6 playoff games he scored 2 goals and 2 assists. After the Generals were eliminated from the 2012 playoffs, Thomas joined the Connecticut Whale of the American Hockey League.
Professional
Thomas signed a professional contract with the Rangers on May 19, 2011. He scored his first professional goal for the Connecticut Whale on April 13, 2012 against the Manchester Monarchs. In five regular season games for the Whale in 2011–12, Thomas scored that one goal and added one assist. He also played for the Whale in the AHL playoffs. On February 23, 2013 Thomas was recalled to the Rangers. Thomas made his NHL debut that night against the Montreal Canadiens in Montreal, and was scoreless with 2 shots on goal in 12 minutes as the Rangers were shut out. Thomas returned to the Whale after the game. He finished the 2012–13 AHL season with 19 goals and 16 assists in 73 games for the Whale. After the 2012–13 Whale season, he was added to the Rangers' playoff roster. On July 2, 2013, Thomas was traded by the Rangers to the Montreal Canadiens in exchange for prospect Danny Kristo. In the 2014–15 season, on February 12, 2015, Thomas scored his first NHL goal against Edmonton Oilers in Montreal, Quebec at the Bell Centre. During the 2015–16 season, on December 15, 2015, Thomas was traded by the Canadiens to the Arizona Coyotes in exchange for prospect Lucas Lessio. He was assigned to AHL affiliate, the Springfield Falcons He was recalled for 2 games before the All-Star Break and appeared in a solitary game with the Coyotes before being returned to the AHL during the All-Star Break. During his first game upon returning to the AHL he suffered a season ending injury which required surgical repair. On July 1, 2016, Thomas signed as a free agent to a one-year, two-way contract with the Washington Capitals. In 65 games with the Bears in the 2016–17 season, Thomas added 24 goals and 49 points. As a free agent in the following off-season, Thomas was unable to secure a NHL contract and later agreed to a one-year AHL deal with the Wilkes-Barre/Scranton Penguins, affiliate to the Pittsburgh Penguins, on September 13, 2017 in order to maintain his Olympic team eligibility. After completing his sixth professional season, Thomas signed his first contract abroad as a free agent, agreeing to a one-year deal with Swedish club, Rögle BK of the Swedish Hockey League, on July 12, 2018. On November 1, 2018, Thomas left the SHL in order to sign a contract for the remainder of the season with Russian outfit, Traktor Chelyabinsk, of the Kontinental Hockey League. In the following 2019–20 season, Thomas continued in the KHL with Chelyabinsk, contributing with just 2 goals and 3 points in 20 games. With Traktor finishing well out of playoff contention, on February 17, 2020, Thomas left the KHL and joined SC Bern of the National League to provide depth for the final playoffs push.
International play
Thomas represented Canada at the 2010 IIHF World U18 Championships. He had two goals and one assist in six games for Team Canada. He was invited to the selection camp for Canada's National Junior Team for the 2012 World Junior Ice Hockey Championships. In November 2017, as part of the Olympic evaluation process, Thomas travelled to Finland as a member of Team Canada to participate in the Karjala Cup. In the final Olympic evaluation tournament, Thomas won the Spengler Cup with Team Canada in Davos, Switzerland on December 31,2017. Thomas was then selected as a member of Canada's team for the 2018 Winter Olympics where he earned the bronze medal.