Werenka played college hockey for the Northern Michigan University Wildcats, with whom he won the 1991 NCAA hockey title. In 1986-87, he enrolled at Northern Michigan University and scored eight points as a WCHA freshman. The following season, he improved to 30 points. In 1988-89, he scored 20 points in 28 games and helped his school win a WCHA championship. After scoring seven points in eight games the following season, he then scored 20 goals and 63 points as a college senior in 1990-91. He was named both a WCHA First Team All-Star and a NCAA West First Team All-American that year. At the NCAA championships, he was named a tournament All-Star.