2008-09: A product of the Pomfret School and the New Hampshire Junior Monarchs junior program, Brian Flynn skated in 38 games for the University of Maine as a freshman. He was the second-leading scorer for the Black Bears behind Red Wings' prospect Gustav Nyquist, scoring 12 goals with 13 assists, And was minus-one with 10 penalty minutes. Five of Flynn's 12 goals were scored on the power play. After winning 10 of 16 games to start the season, Maine struggled in the second half; finishing seventh in Hockey East.
2009-10: The line of Flynn, Nyquist and Tanner House was again the top scoring line in Flynn's sophomore season as the three finished 1-2-3 in scoring for the Black Bears. Flynn was second behind Nyquist with 47 points – scoring 19 goals with 28 assists in 39 games – and was plus-seven with 12 penalty minutes. Maine was much-improved, finishing fourth in Hockey East and advancing to the conference playoff championship game. The Black Bears lost to eventual national champion Boston College in a wild 7-6 overtime game in the final. Flynn assisted on two goals in that game – including Joey Diamond's game-tying goal with 27 seconds remaining.
2010-11: Flynn led the University of Maine in goals as a junior – scoring 20 for the first time in his college career – and finished fourth on the Black Bears with 36 points (behind Nyquist (51) and Spencer Abbott (40)). He finished plus-five with 8 penalty minutes in 36 games and was awarded Hockey East's Sportsmanship Award. Maine finished fifth in Hockey East and lost to Merrimack in the conference quarterfinals.
2011-12: Flynn signed a one-year entry-level contract with the Sabres in March 2012 following his senior season at Maine and made his pro hockey debut with AHL Rochester. He was minus-2 with 1 assist and 2 penalty minutes in five games with the Americans and did not play in their playoff series with Toronto. Flynn was the second-leading scorer for Maine behind Abbott, scoring 18 goals with a career-high 30 assists, and was plus-18 with 37 penalty minutes in 40 games. Maine finished fourth in Hockey East and faced Boston College in the playoff championship game for the second time in three years. The Black Bears received first NCAA tournament berth since 2006-07.
Flynn will develop with in the AHL with Rochester in 2012-13.