In March 2011, Atkinson signed a two-year contract with the Columbus Blue Jackets. He then began playing for the Springfield Falcons, the Blue Jackets’ American Hockey League (AHL) affiliate. While with the Falcons, Atkinson made his mark on the team by recording three goals and two assists for five points in five games.

His first NHL goal was scored on October 10, 2011, against Cory Schneider of the Vancouver Canucks, a game the Canucks won 3–2. He was returned to Springfield after playing four games with Columbus in the 2011–12 NHL season.

After his return to the AHL, Atkinson was named to the 2012 AHL Eastern Conference All-Star Team on January 4, 2012, as a result of his impressive play with Springfield during the 2011–12 AHL season, with 15 goals and ten assists through 30 games. He was one of 13 rookies named to the two All-Star teams.

On April 5, 2012, Atkinson recorded his first career NHL hat-trick against the Colorado Avalanche in a 5–2 Blue Jacket win. Atkinson recorded his second hat trick against the Chicago Blackhawks to help the Blue Jackets win 5–2 on March 27, 2015. Atkinson recorded his third career hat trick during the 2015–16 season in a 5–2 win over the Montreal Canadiens.

On November 16, 2017, the Blue Jackets signed Atkinson to a seven-year, $41.125 million contract extension worth $5.875 million annually. During the 2017–18 season Atkinson recorded his fourth hat trick against the Philadelphia Flyers to help the Blue Jackets win their sixth straight game.