Fitzgerald, 31, an All-America middle linebacker at Northwestern when the Cats won back-to-back Big Ten Championships in 1995-96, joined Walker's staff as a defensive secondary coach in 2001. He was named linebackers coach in 2002 and became the program's recruiting coordinator in 2004.
"It's a dream of mine to be the head football coach here, but not under these circumstances," Fitzgerald said. Walker died of a heart attack on June 29 at 52 and was buried Thursday.
Northwestern Athletic Director Mark Murphy said with the season starting next month there was no time to conduct a full-time search for a successor for Walker and he did not want an interim coach.
"One person really stood out and that's Pat Fitzgerald," he said.
Fitzgerald, who becomes the youngest head coach in NCAA Division 1-A, was a defensive coach at Maryland in 1998 and in 1999 at Colorado, and coached at Idaho.
"This would have been Randy's choice," Walker's wife, Tammy, told the Chicago Tribune.