MacIntyre, 53, was fired last month after six seasons as the Buffaloes' head coach. His ouster came on the heels of six consecutive losses, but he guided Colorado to the Pac-12 championship game and earned AP College Football Coach of the Year honors in 2016. He was 30-44 overall as the Buffs' head coach.
MacIntyre worked on the Ole Miss staff from 1999 through 2002 under David Cutcliffe, and on that same staff during the 2002 season was current Ole Miss head coach Matt Luke. MacIntyre and Luke also worked together on the Duke staff for two seasons in 2008-09.
MacIntyre, the son of former Vanderbilt head coach George MacIntryre, replaces Wesley McGriff, who was fired in November.