He played in Major League Baseball (MLB) for the Seattle Mariners, Atlanta Braves, Oakland Athletics, and New York Mets.

The Seattle Mariners selected O'Flaherty in the sixth round of the 2003 Major League Baseball Draft.

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 next day, however, infielder Greg Dobbs was returned to Triple-A, allowing O'Flaherty to pitch his first major league game.

[5] On April 7, 2009, O'Flaherty made his Braves debut, pitching 1+1⁄3 scoreless innings and allowing one hit.

He spent the entire 2009 season on the active roster and finished the year with a 3.04 ERA, a 1.243 WHIP, and a 39-to-18 strikeout-to-walk ratio in 56+1⁄3 innings.

O'Flaherty served as an important part of the Braves bullpen during the 2011 season where he pitched primarily during the 7th inning.

[14] The New York Mets acquired O'Flaherty and cash considerations for a player to be named later, minor league pitcher Darwin Frias, on August 4, 2015.

[18] O'Flaherty pitched to a 6.91 ERA in 39 games, and spent two stints on the disabled list, the first time for a strained knee.

His pitch selection did not vary greatly between right-handed and left-handed hitters, although lefties tended to see fewer sinkers and more sliders.