The 38-year-old Conlin helped Yale win this year's Ivy League title in his sixth season. He spent the final four years as offensive coordinator and associate head coach.
This year's offense ranked 12th in the FCS in total offense (450.7 yards per game).
"We believe he is one of the top young coaches in the country who truly cares about the welfare of the student-athlete which makes him a perfect fit for Fordham," athletic director Dave Roach said.
Conlin also was an assistant coach at Harvard, New Hampshire and West Virginia Tech. He was a three-year starter at defensive tackle for the University of Pittsburgh.