Oakland Raiders After going undrafted in the
2015 NFL draft, Fajardo signed with the
Oakland Raiders on May 8, 2015. On September 1, he was waived by the Raiders.
Toronto Argonauts On October 8, 2015, Fajardo was signed to the practice roster of the
Toronto Argonauts of the
Canadian Football League. He re-signed with the Argonauts on May 17, 2016. Fajardo scored his first professional rushing touchdown on July 13, 2016, before throwing his first professional touchdown pass on July 25, 2016. Fajardo's role expanded in 2017 into a change-of-pace backup while starter
Ricky Ray was injured. After Ray returned, Fajardo returned to his role as
short-yardage quarterback. He scored the game-winning touchdown with 23 seconds remaining in the
2017 East Final in short-yardage on a 1-yard plunge against the
Saskatchewan Roughriders, sending the Argonauts to the
105th Grey Cup game. The Argos won the championship game over the
Calgary Stampeders. Although Fajardo showed considerable promise and poise when he played, the Argonauts were unable to sign him to a contract extension with the acquisition of
James Franklin from the
Edmonton Eskimos.
BC Lions After entering free agency, Fajardo signed with the
BC Lions on February 16, 2018. Fajardo continued his role as a short down rusher and change of pace quarterback behind
Travis Lulay and
Jonathon Jennings, registering 14 completions on 20 attempts for 153 yards, one touchdown, and one interception, as well as 42 rushes for 108 yards and 5 more scores.
Saskatchewan Roughriders On the third day of free agency in 2019, Fajardo signed with the
Saskatchewan Roughriders on a one-year contract, joining a quarterback room featuring
Zach Collaros and
David Watford. Fajardo became the starting quarterback following an injury to Collaros in the opening game of the season. Fajardo threw for 360 yards in his first start for the Roughriders, setting a franchise record for most yards in a first start. He led the team to a win on July 1, 2019, throwing for 430 yards against the
Toronto Argonauts. Fajardo continued to play well in the following weeks which prompted the Roughriders to trade Collaros to the Argonauts, solidifying their trust in Fajardo. On October 21, 2019. Fajardo agreed to a two-year contract extension with Saskatchewan. He signed a contract extension through the 2022 season with the team on January 5, 2021. Fajardo remained the starting quarterback for the Riders in 2021, leading the team to 9–5 record and secured a home playoff match against rival
Calgary Stampeders, whom they defeated 33–30 in overtime despite Fajardo throwing four interceptions. The Riders were defeated in the Western Final by the eventual champions the
Winnipeg Blue Bombers. On January 31, 2022, Fajardo and the Roughriders agreed to a restructured contract for the
2022 season. After starting the season with four wins in their first five games the season proved to be challenging for Fajardo and the Riders as the team would go on to lose nine of their next 11 matches, culminating in Fajardo being benched for the Riders penultimate match. On February 13, 2023, one day before becoming a free agent, Fajardo posted on Twitter announcing that he would not be returning to Saskatchewan.
Montreal Alouettes On the first day of free agency Fajardo signed a two-year contract with the
Montreal Alouettes. Coincidentally,
Trevor Harris, the Alouettes' starter in 2022, replaced Fajardo in Saskatchewan. Fajardo had a 9–7 record as a starter and helped the Alouettes to a playoff spot as runners-up in the East Division. The Alouettes reached the
110th Grey Cup, in which Fajardo was named the game's
Most Valuable Player. He threw three touchdowns in the championship game, including the winning score to
Tyson Philpot with 13 seconds remaining. Fajardo returned as the Alouettes' starter in 2024, winning his first five games before suffering an injury in the team's sixth game against the
Toronto Argonauts. Fajardo missed the next four games before returning to the starting role, sharing starts and playing time with
Davis Alexander as the Alouettes went 12–5–1 and received a bye to the East Final. In the East Final, Fajardo threw for 330 yards and three touchdowns but was also intercepted twice and lost a fumble as the Alouettes lost 30–28 to the Argonauts. Following the season, Alexander was given a three-year extension, signaling the Alouettes' commitment to move on from Fajardo as their starter.
Edmonton Elks On December 17, 2024, it was announced that Fajardo had been traded to the
Edmonton Elks in exchange for
McLeod Bethel-Thompson. Fajardo began the 2025 season as the short-yardage quarterback and the backup to starter
Tre Ford. After the Elks began the year with a 1–4 record, Fajardo was named the starter; he started the remaining 13 games, going 6–7 as a starter and passing for 3,408 yards, 14 touchdowns and 7 interceptions. ==Career statistics==