The Florida Panthers made Bartkowski, a Pittsburgh-born defenseman, their seventh-round pick (No. 190) in the 2008 NHL Draft. But he never played for Florida. Bartkowski was in his second season with Ohio State when the Panthers traded him to the Boston Bruins on March 3, 2010. He signed a two-year entry-level contract with the Bruins on April 29, 2010.

Bartkowski made his NHL debut on Jan. 10, 2011, helping the Bruins defeat his hometown team, the Pittsburgh Penguins, 4-2. He played six regular-season games and was with the Bruins for their run to the Stanley Cup, though he didn't dress for any Stanley Cup Playoff games.He spent most of the next two seasons with Providence of the American Hockey League, but played 11 regular-season games and seven playoff games for Boston in 2013, scoring his first NHL goal during Boston's victory against the Toronto Maple Leafs in Game 7 of the Eastern Conference Quarterfinals.

Bartkowski spent the next two seasons with the Bruins before signing with the Vancouver Canucks on July 1, 2015. He scored his first regular-season goal (in his 137th game) on Oct. 18, 2015, and finished with 18 points (six goals, 12 assists) in 80 games but wasn't re-signed. After spending the first half of the season back with Providence, he signed with the Calgary Flames on Feb. 15, 2017, reuniting him with coach Glen Gulutzan, who had been an assistant during his time in Vancouver.