For the 1959 CFL season, Kapp joined the Calgary Stampeders of the CFL. Then for the 1960 CFL season, Kapp led the Calgary Stampeders to their first playoff appearance in years. The season was a difficult one, because he injured his knee against the Toronto Argonauts early in the season, but did not miss any games, because he played heavily taped.
In 1961, the B.C. Lions, then the CFL's newest franchise, traded four starting players to the Calgary Stampeders for Joe Kapp. The move paid off for the Lions when Kapp led the team to a Grey Cup appearance in 1963. While the following season, Kapp led the Lions to their first Grey Cup victory in 1964. However, the Lions proved unable to defend their championship in 1965.
By that time, Joe Kapp had proven he was an elite quarterback, and also developed the reputation of being a tough player and a great leader. While most quarterbacks dislike being hit, Kapp was the opposite. He loved to hit and when he took off on a run he’d try to run over defenders.
Before the 1967 season, Joe Kapp made the decision to play in the NFL. The Oakland Raiders, San Diego Chargers, and Houston Oilers were heavily pursuing him. Kapp decided to sign a contract with the Houston Oilers, but the B.C. Lions and the CFL complained to Pete Rozelle, the NFL’s commissioner accusing the Houston Oilers of tampering. Rozelle after his investigation, announced the Houston Oilers had indeed tampered by signing Kapp while he was under contract to the B.C. Lions, so he voided the contract.
Kapp ended up signing with the NFL's Minnesota Vikings in a multi-player "trade" between the CFL and NFL teams, one of the very few transactions to ever occur between the two leagues.
The Minnesota Vikings in 1965 had drafted running back Jim Young out of Queens University in Kingston, Ontario. He had spent the 1965 and 1966 seasons with the Vikings, but wanted to return to Canada. The B.C. Lions were very interested in acquiring Young , however the Toronto Argonauts had his CFL rights.
The Minnesota Vikings general manager was Jim Finks, who had brought Kapp to Canada in 1959, and their head coach was Bud Grant who had faced Kapp while coaching the Winnipeg Blue Bombers. Both Finks and Grant thought Joe Kapp would be the best replacement for Fran Tarkenton who had been traded to the New York Giants. To make this transaction possible, the B.C. Lions traded all-star defensive lineman Dick Fouts, and future CFL Hall of Fame running back Bill Symons to the Toronto Argonauts for the CFL rights to future CFL Hall of Fame wide receiver Jim Young. They then managed getting Kapp waived out of the CFL.
Kapp, waived from the CFL, was free to sign with the Minnesota Vikings, who had previously claimed his NFL playing rights from the Washington Redskins. On the other hand, Jim Young waived from the NFL signed with the B.C. Lions.
Prior to the 1969 season, the Minnesota Vikings had exercised the option clause of his contract, so Kapp had played the entire season without a new contract. It was unusual and unprecedented for teams to use the team’s option and not to offer a new contract prior to a season. This dispute made him a free agent for the 1970 season, by the NFL's own rules.
Inspite of being a Super Bowl quarterback, no teams in the NFL made contact with Kapp until September of the 1970 season, when the Boston Patriots signed him to a four-year contract, making him the highest paid player in the league. Pete Rozelle stepped in and forced the Boston Patriots to give up two number one draft picks as compensation to the Minnesota Vikings.
The Boston Patriots of 1970 were a poor-performing team and Kapp played poorly himself that season, leading the team to the league's worst record. When the year ended Pete Rozelle demanded that Kapp sign what is called a Standard Player Contract. After conferring with his lawyer and the NFL Players Association, Kapp refused to sign a new contract.
Kapp started an anti trust lawsuit vs. the NFL claiming the standard NFL contract was unconstitutional and a restraint of trade. He won the Summary Judgment after four years. The court had ruled that Joe Kapp’s trade was indeed restrained. It was two years later (April 1, 1976) in the trial for damages, that the jury decided that Kapp was not damaged.
Although Kapp was not awarded any damages, in 1977 the rules at issue in the Kapp case were later revised, a new system was instituted, and a multi-million dollar settlement was made between the NFL and the NFL Players Association.
In December of 1981, Kapp made a promise to the football team that he would not consume any of his favorite alcoholic beverage, tequila, until the Golden Bears reached the Rose Bowl. As of October 2007, the Golden Bears have yet to return to the Rose Bowl and Kapp has resorted to drinking rum instead.
Kapp was the coach during The Play, the famous five-lateral kickoff return by the Cal team to score the winning touchdown on the final play of the 1982 Big Game against arch rival Stanford University.
During the 1986 College football season, the Bears lost to Boston College, defeated Washington State, then lost to San Jose State. Following an embarrassing 50-18 loss at Washington on October 4th, Kapp expressed frustration unzipping his pants in front of the Seattle media. He was notified that he would be released after the 1986 Big Game. The Bears responded by beating the #16 ranked and Gator Bowl bound Cardinal 17-11. This gave Kapp a 3-2 record in the big game. He was carried out of the stadium amid chanting from the student section, "We Want Kapp!", echoing a cheer from his playing days with the Boston Patriots.