On January 13, 2011, Pasqualoni was hired to lead the University of Connecticut football program, by soon to be dismissed AD Jeff Hathaway, two weeks after former coach Randy Edsall left for the University of Maryland. His two full seasons saw identical records of 5–7 — only his second and third losing seasons as a Division I-A/FBS head coach. He was dismissed as coach of the Huskies on September 30, 2013 in the midst of his 3rd season after starting 0–4.