O'Flaherty became the first Mariner in franchise history to begin his major league career with seven straight wins.
O'Flaherty quickly made his way through the Mariners' minor league affiliate teams. He started 2006 with the Single-A Inland Empire 66ers where he had a 3.45 ERA and struck out 33 batters in 16 relief appearances. On May 27, he moved to the Doulble-A San Antonio Missions where he had a record of 2-2 with an ERA of 1.14 and seven saves in 25 games. He moved again that same season to the Triple-A Tacoma Rainiers on August 9; he would stay with them until his August 16 appearance with the Mariners. His combined minor league record in 2006 was 3-3 with a 2.01 ERA, eight saves, and 73 strikeouts in 43 games.
On the same day of O'Flaherty's debut, the Seattle Times reported that his "big-league visit was too short to qualify as a cup of coffee". The night before he had been flown in from Triple-A Tacoma in order to replace a seemingly injured Rafael Soriano. When O'Flaherty arrived, Soriano convinced coaches he was healthy enough to remain on the Mariners' roster, so O'Flaherty was sidelined out of uniform for the rest of the night. The next day, however, infielder Greg Dobbs was returned to Triple-A, allowing O'Flaherty to pitch his first major league game.
During his debut season in 2006, O'Flaherty faced some challenges: however, his pitching became more refined in the season and O'Flaherty quickly become a mainstay relief pitcher for the Mariners. Things went downhill for him in . In 7 games for the Mariners, O'Flaherty gave up 15 earned runs for a 20.25 ERA and was optioned to the minors.