Carey got the nod to lead the Huskies on the same day it was announced the Mid-American Conference program would play in the Jan. 1 Orange Bowl against Florida State.
Carey will lead NIU in the contest -- the first-ever BCS bowl appearance for the school.
Doeren tendered his resignation Saturday to take over the vacant head coaching job at North Carolina State.
"What we need in our program is consistency and stability, and I believe that Rod brings that," Northern Illinois Director of Athletics Jeff Compher said. "This will allow us to stay on our current trajectory as a nationally prominent program."
Carey, a native of Wayzata, Minn., served as an assistant under Doeren for two years. He took over as offensive coordinator after Mike Dunbar resigned for health reasons following the first game.