Paopao began his CFL career as a quarterback for the BC Lions in 1978. He was nicknamed the "Throwin' Samoan" for his great ability to pass, as he led the Lions in passing for the next three seasons and set a CFL record in 1979 for pass completions in a single game. By 1983, he had lost the starting job to Roy Dewalt. In 1984 he signed with the Saskatchewan Roughriders and again led that team in passing. He was traded to the Ottawa Rough Riders in 1987, and the following year to the Winnipeg Blue Bombers. That year he was named the offensive backfield coach of the BC Lions, thus beginning his CFL coaching career. The next year however, he went back to his old position of quarterback for the Lions, backing up Doug Flutie, in his last season.
In 1991, Paopao was made the quarterback coach of the Lions. In 1992 he was made their offensive co-ordinator where he remained until becoming the offensive co-ordinator of the Edmonton Eskimos in 1994. In 1996 Paopao became head coach of the Lions, but later found himself as offensive co-ordinator once again, this time for the Blue Bombers. He went back to the Lions in 1999 and was made assistant head coach. In 2001 he found himself as the offensive co-ordinator of the San Francisco Demons of the XFL. That league only lasted one season, and he was later picked up by the new Renegades franchise in Ottawa where he coached from 2002–2005, compiling a 23 Win-49 Loss record. Paopao was then hired by the Hamilton Tiger-Cats and named offensive co-ordinator for the 2006 season. He was later relieved of his duties with the Tiger-Cats on August 28, 2006.
On February 6, 2014, the BC Lions announced Paopao would be re-joining the organization as its receivers coach.
Paopao joined the University of WaterlooWarriors as the team's offensive coordinator and assistant head coach in 2007, a position he would hold for five years. He was named the team's interim head coach for the 2012 season after Dennis McPhee's resignation, and then full-time head coach in February 2013. In two seasons with the Warriors, Paopao had a 3-13 record. Paopao left Waterloo in February 2014 to join the BC Lions as receivers coach. On March 27, 2015 Joe Paopao was named offensive coordinator of the Simon Fraser University Clan football team in the NCAA's Division II Great Northwest Athletic Conference.