He attended Yale College, where he obtained a B.A. in 1735. He married Esther Edwards, daughter of the New England Divine Jonathan Edwards and his wife Sarah, daughter of Rev. James Pierpont.
At a time when the Yale Corporation, of which he was a member, was split regarding the disciplines introduced by Yale's first President, Rev. Thomas Clap, Jonathan Edwards, Rev. Aaron Burr, and Jonathan Dickinson , in opposition to Clap, left New Haven, Connecticut for Newark, New Jersey, and later founded the College of New Jersey, (now Princeton University) in 1746.
Rev. Burr was the second president (1748—1757) of the College.