Lynch finished with 223 yards on 20 of 33 passing and threw touchdown passes of nine and four yards.
Northern Illinois (7-1, 4-1) held a 13-7 lead before Lynch’s 15-yard touchdown run gave the Huskies a 20-7 advantage at halftime.
After Lynch’s second touchdown pass pushed the lead to 30-7, his second touchdown run, this time a 35-yarder, created the final margin.
Lynch, who finished with 131 yards on the ground, has rushed for 100-plus yards in each of the Huskies’ last six games.
Akron (1-7, 0-4) struggled to move the ball, gaining just 194 yards on 65 plays from scrimmage.
Northern Illinois has won 16 of its last 17 games. Its last lost was by one point to Iowa in the 2012 season opener.