In the early 1990's, about the same time that the college made the decision to increase enrollment, the Commons system was formed. The idea behind the commons system was a way to preserve the small college camaraderie that had always characterized Middlebury while at the same time creating what then President John M. McCardell described as “seamlessness” between academic and residential life.

Ezra Brainerd Commons is named for Ezra Brainerd, who became president of Middlebury College in 1885. He was born in St. Albans, Vermont, and attended Middlebury College as a student, graduating with the class of 1864. After graduating from theological school, Brainerd returned to Middlebury where he taught in virtually every department—English and rhetoric, physics and mathematics—and distinguished himself as a botanist, studying primarily violets and blackberries. Under his leadership the college came from near extinction to modest prosperity. Women were admitted and began graduating during his tenure. Starr Library was built during his presidency, as was Warner Hall. On the 50th anniversary of his graduation, Mead Chapel was started, with funds solicited from Brainerd's classmate John A. Mead.
Former Faculty Heads of Brainerd are Robert Osborne, Kirsten Hoving, Paul and Jennifer Nelson and Karl Lindholm.