On September 29, 2009, Ottawa announced that Carkner had made the team's roster, as he spent the entire 2009-10 season in the NHL. In 81 games, he had two goals, 11 points, and 190 penalty minutes, helping Ottawa reach the playoffs. He scored his first NHL goal three games into the season, scoring on New York Islanders goaltender Martin Biron in the second period of a 3–2 Senators victory. In the playoffs, he had a memorable triple-overtime goal in Game 5 of the Eastern Conference quarter-finals against Marc-André Fleury and the Pittsburgh Penguins; that was the only point Carkner earned while appearing in all six games as the Penguins took the series win. He appeared in 50 games with Ottawa in the 2010-11 season, scoring a goal and seven points, as well as earning 136 penalty minutes.