In college, he played for the University of Cebu Webmasters. He is the primary factor for leading his team to win the Cebu Schools Athletic Foundation, Inc. (CESAFI) crown. Junmar Fajardo also played for three Philippine Collegiate Championship League (PCCL) tournaments which pitted his team from the best college teams from National Collegiate Association (NCAA) and University Athletic Association of the Philippines (UAAP).
During the 2008 PCCL tournament, he scored 24 points, hauled 12 rebounds and blocked 9 shots against the tough Letran Knights with Dennis Daa delivering with 27 points. In 2009, University of Cebu Webmasters met the powerhouse University of the East Red Warriors that featured Elmer Espiritu. He also played well against these guys and contributed 24 points. The 2010 tournament gave Fajardo the opportunity to play against the Ateneo Blue Eagles and De La Salle Green Archers. He delivered a monster performance against the Eagles by putting 30 points and grabbing 15 rebounds. Against the Archers, he scored 16 points, 21 rebounds and 5 blocks. In his three PCCL tournaments career, he averaged 23.5 points per game against the best college teams in the Philippines.
He currently has an average of 4.57 points, 4.14 rebounds, 0.62 assist while shooting 52.11 percent in the field for the San Miguel Beermen. He declared himself available for the PBA 2012 draft and Petron Blazers already proclaiming of picking him and making him the first pick of this talented draft class which also features Chris Tiu, Calvin Abueva, and PBA D-League players like Chris Ellis as well as Cliff Hodge.