He played center for the University of Cebu Webmasters in the CESAFI and for the San Miguel Beermen in the ASEAN Basketball League before being selected as the first overall in the 2012 PBA draft by Petron Blaze Boosters.

In the semifinals of the 2013 PBA Governors' Cup against Rain or Shine, Fajardo scored 26 points in Game 2 who held up his own against opposing big men Beau Belga and J.R. Quiñahan.

He led the Best Player of the Conference race with averages of 21.8 points, 16 rebounds, 1.4 assists and 1.4 blocks, but his team lost to eventual champion San Mig Super Coffee in the quarterfinals.

The second-seeded Beermen defeated Rain or Shine in five games in the semifinals before asserting their mastery against Alaska by sweeping them in the Finals and win the Governors Cup which marks their 21st title in franchise history.

In Fajardo's absence, many stepped up including players on the bench and managed to squeak a come-from-behind win in Game 4 after being down 0–3 in their Finals rematch against Alaska.

Fajardo conspired with teammate and former MVP Arwind Santos in the title-clinching win, scoring 21 points each in Game 5 to capture the Perpetual trophy.

With the help of Best Import awardee Charles Rhodes along with Best Player of the Conference Chris Ross, Fajardo aided the Beermen to capture the second seed and eventually win their second consecutive championship of the season by conquering the 2017 PBA Commissioner's Cup after defeating TNT in six games.

[15] Due to import problems, the Beermen only managed to snag the sixth seed after a costly 101–104 loss against Meralco in the last game of the elimination round, giving them a twice-to-win disadvantage against eventual champions Barangay Ginebra which thwarted their Grand Slam bid in the quarterfinals.

As the Beermen was out of title hunt, Fajardo lost the BPC award to rival big man Greg Slaughter despite leading the statistical points.

[17] Fajardo remained unstoppable in the 2017-18 PBA Philippine Cup, averaging league-high 22.8 points along with 13.3 rebounds, 1.8 assists and 2.1 blocks to lead the Beermen to the top seed once again.

He shattered record books by extending his reign as the Best Player of the Conference of the Philippine Cup for the fourth consecutive season, his sixth overall which is the most in league history.

[18] The Beermen avenged their painful loss against Barangay Ginebra the previous conference which foiled their Grand Slam bid through a gentleman sweep in the semifinals.

Despite only finishing sixth after the elimination round, the defending champion Beermen maneuvered their way into the Finals with the help of import Renaldo Balkman to set a date against sister team Barangay Ginebra.

He returned deep into the elimination round in a win against Rain or Shine, where the Beermen finished as the sixth seed but eventually lost to twice-to-beat Alaska in the quarterfinals.

Fajardo rewrote history books once again after receiving his fifth straight Most Valuable Player award after winning back-to-back BPCs in the first two conferences despite missing the majority of the Governors' Cup due to injury.

[21] The Beermen was in unfamiliar territory after finishing seventh seed in the 2019 PBA Commissioner's Cup with a 5–6 record as the returning former Best Import Rhodes struggled, which was eventually replaced by Chris McCullough later in the conference.

[22] In the 2019 PBA Governors' Cup and another Grand Slam conquest at hand, Fajardo led once again in the Best Player of the Conference race with averages of 18.9 points, 13.6 rebounds, 1.9 assists and 1.2 blocks per game.

Despite leading the BPC race, Fajardo lost the award to former teammate Christian Standhardinger after San Miguel's early exit and another failed Grand Slam bid.

With Fajardo's absence, along with the injury of all-star teammate Terrence Romeo, the defending champion Beermen was eliminated by Meralco in the quarterfinals of the 2020 PBA Philippine Cup, ending their five-year reign.

Though still struggling and visibly adjusting from basketball play, he still made respectable averages of 13.5 points, 10.8 rebounds, 2.2 assists and 1.1 blocks in the 2021 PBA Philippine Cup which is still good enough for finishing fifth in the Best Player of the Conference race by which he won the previous six times prior to his injury.

[25] The Beermen lost in the semifinals against the TNT Tropang Giga in seven games in the semi-bubble held in Don Honorio Ventura State University gymnasium.

He went on to win his fourth Finals MVP award with averages of 19.0 points, 16.6 rebounds, 2.7 assists and 1.1 blocks, tying James Yap, LA Tenorio and Danny Seigle for the most in league history.

[32] In his first game in international competition, Fajardo scored 2 points, grabbed 2 rebounds, and was called for 4 personal fouls in less than 9 minutes of action against Saudi Arabia.

During his stint in the 2014 FIBA World Cup, Fajardo was consistent in his limited minutes on the court while providing energy and hustle coming off the bench as a reliever for Blatche.

Fajardo had 15 points, 9 rebounds, 2 steals and 2 assists as he provided hustle and muscle against the big men of Senegal most especially in the final quarter of regulation and overtime when Blatche was fouled out.