Brannagan began his university football career with the Queen's Golden Gaels in 2005 and quickly assumed the starting quarterback position.
In a game against Wilfrid Laurier, he came off the bench in the fourth quarter and threw for 110 yards, earning the start the following week against York University.
[1] In a week six win versus the University of Ottawa, he passed Tommy Denison as Queen's all-time leading passer.
In the post-season, Brannagan was named Yates Cup MVP after recording a 43–39 win over Michael Faulds and the Western Ontario Mustangs.
He capped off his outstanding collegiate career with a 33–31 win over the Calgary Dinos in the Vanier Cup where he was again named MVP for the game.
After impressing at the 2010 CFL E-Camp, Brannagan was signed by the Toronto Argonauts the day after the camp ended, on March 15, 2010, to a three-year contract.