Kowalczyk attended Westfield High School, where he earned four letters in football and baseball, three in basketball and two in track. In football and baseball he was named to the All-state team twice. He won the state 100-yard dash title twice. As a senior, he received the Harry Agganis Award as the best high school athlete in New England.
He accepted a scholarship from Michigan State University, where he became a three-year starter at right halfback. As a sophomore he was given the nickname "The Sprinting Blacksmith", after his efforts helped his team defeat UCLA in the 1956 Rose Bowl. He recorded 584 yards and 6 touchdowns in the season.
As a junior he was limited with a serious ankle sprain he suffered during fall practice and only registered 128 yards and 2 touchdowns.
In 1957, he posted 545 rushing yards (5.4 yards average), 9 touchdowns and 7 receptions for 128 yards. He placed third in the Heisman Trophy voting. He finished his career with 1,257 rushing yards on 225 carries, 16 touchdowns, 10 receptions for 187 yards and one touchdown.
Kowalczyk spent six weeks with the Detroit Lions in training camp, before his rights were sold to the Dallas Cowboys. Although he initially refused to report to the team, he changed his mind after commissioner Pete Rozelle threatened to fine him.
He became the first starting fullback in franchise history (7 starts), while sharing playing time with Gene Babb (5 starts). He finished with 50 carries for 156 yards (third on the team) and 14 receptions for 143 yards (fifth on the team). He was waived in on September 12, 1961.