Kowalczyk spent eight seasons at Wisconsin-Green Bay where he had a 136-112 record and put together consecutive 22-win seasons the last two years.
Wisconsin-Green Bay had three straight losing seasons before Kowalczyk arrived.
Toledo athletic director Mike O'Brien said Tuesday that Kowalczyk has proved that he can build a program.
He replaces Gene Cross who resigned after just two seasons. The Rockets finished 4-28 overall and 1-15 in the Mid-American Conference this season.
The Rockets haven't been to the NCAA tournament since 1980.