In March 2010, Wesleyan hired Whalen as its head football coach and assistant athletic director. At the time, Whalen told reporters, "This would have never, ever, ever happened if I didn't go here. That was a big, big draw for me, to come home, to come back to Wesleyan and see if we can put this thing back on track." In his first year at Wesleyan, Whalen finished the year 4–4, losing close games to Middlebury, 24–21, and Trinity, 27–20, while also losing to Little Three rivals Williams and Amherst.