Cowen began the 2012-13 season with the Binghamton Senators, recording three assists in three games. He underwent surgery in November to repair a torn labrum in his left hip, sidelining him until April when he made his NHL season debut against the Carolina Hurricanes.
The 22-year-old Cowen played seven regular-season NHL games last season, scoring one goal. He also played in each of Ottawa's 10 playoff games against the Montreal Canadiens and Pittsburgh Penguins, recording three assists and 21 penalty minutes.
Cowen missed the start of training camp as his contract negotiations dragged.
"It's great, you go through a hard negotiation and things are said, but we obviously love this guy as a player, as a person, he's what we want," Senators assistant general manager Tim Murray said. "He's kind of a poster boy of what we want here. He works extremely hard, he's low maintenance, he plays hard, he competes, we love him as a player.
"I'm just happy it's over and I hope he's as happy as we are."
Cowen was the Senators' first-round pick (ninth overall) in the 2009 NHL draft.
He played in all 82 games of his rookie season with the Senators in 2011-12, scoring five goals and adding 12 assists.