Prefontaine was born to a French Canadian father and a Vietnamese mother at the Marine Corps Base Camp Pendleton in California.

He returned to the United States and attended El Camino High School in San Diego County, California.

[1] He was named San Diego Tribune Athlete of the Year for North County as a senior and led El Camino High School to a 22–2 record and a CIF Championship as their starting quarterback.

[2] Prefontaine hoped to play quarterback in college football but could only obtain a scholarship as a punter at California State University, Fullerton.

He was officially listed as the team's third-string quarterback (behind Tommy Maddox and Scott Milanovich, the latter of whom would eventually become Prefontaine's coach in Toronto) in order to collect a higher salary and because the XFL did not reserve separate roster spots for punters (on the other XFL teams, placekickers doubled as punters).