[5] He was redshirted during the 2010 season as Colin Kaepernick completed a four-year run as the starting quarterback for the Nevada Wolf Pack football team.

As a redshirt freshman, Fajardo became the starting quarterback for 2011 Nevada Wolf Pack football team.

[11] On October 8, 2015, Fajardo was signed to the practice roster of the Toronto Argonauts of the Canadian Football League.

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.

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.

On the third day of free agency in 2019, Fajardo signed with the Saskatchewan Roughriders on a one-year contract,[17] joining a quarterback room featuring Zach Collaros and David Watford.

[25] On February 13, 2023, one day before becoming a free agent, Fajardo posted on Twitter announcing that he would not be returning to 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.

He threw three touchdowns in the championship game, including the winning score to Tyson Philpot with 13 seconds remaining.

Following the season, Alexander was given a three-year extension, signaling the Alouettes' commitment to move on from Fajardo as their starter.