2005 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. He threw for 341 yards in the team's win and never looked back, starting the final seven games of the season. He was named the
OUA Rookie of the Year for the 2005 season after completing 115 passes out of 209 attempts for 1,860 yards to go along with 12 touchdowns and 10 interceptions.
2006-2007 In 2006, Brannagan started all ten games for Queen's (including two playoff games), leading the team to a 4–4 record. He finished the season ranked third in the OUA with 1,744 passing yards and threw for 11 touchdowns and 11 interceptions. Heading into the final week of the 2009 regular season and despite having already missed a game due to injury, Brannagan led Western quarterback Michael Faulds by 164 career passing yards, and sat just 30 yards short of the all-time CIS record of 10,455 yards which was set just one season earlier by former
McGill quarterback Matt Connell. However, Brannagan had a mediocre Week 8, completing 25 of 45 attempts for 289 yards and no touchdowns, while Faulds threw for an impressive 550 yards against the
University of Toronto. Brannagan subsequently finished second on the all-time list with 10,714 yards, having been surpassed by Faulds, who finished with the record of 10,811 yards. ==Professional career==