Howie Dickenman saw Mojica at a tryout camp in New Jersey after his graduation from high school in 2003, and offered him scholarship to play for Blue Devils. the Mojica played college basketball for Central Connecticut Blue Devils men's basketball, In his freshman season, he averaged 7.9 points, 2.9 rebounds and 1.3 assists. In his sophomore year, he averaged 9.9 points, 4.5 rebounds and 2.5 assists. In his Junior year, he averaged 8.9 points, 4.6 rebounds and 1.8 assists. In his Senior year, he averaged 16.8 points, 7.9 rebounds and 3.2 assists.
Professional career
Mojica started his professional career at Poland with the AZS Koszalinbasketball team in the 2008–09 season. He averaged 16.6 points, 4 rebounds and 1.6 assists while he was there.In the 2008–09 season, Mojica moved to the Puerto-Rican side Vaqueros de Bayamón, in his first season there, He averaged 12.4 points, 4.5 rebounds and 2.4 assists. In his second season at Vaqueros de Bayamón, he averaged 12.4 points, 5.9 rebounds and 3.4 assists. in the 2009–10 season, he moved to the Belgian side B.C. Oostende, where he averaged 6.4 points, 2.9 rebounds and 1.8 assists having played 10 games for the team. He moved back to Vaqueros de Bayamón at the 2010–11 season, in that season he averaged 12.5 points, 5.4 rebounds and 2.3 assists. In the next season at Vaqueros de Bayamón, he averaged 12.2 points, 3.8 rebounds and 2.1 assists. In the same 2011–12 season, he moved to Estudiantes de Bahía Blanca in Argentina, where he averaged 15.6 points, 5.6 rebounds and 1.4 assists. In the 2012–13 season, he played for Quimsa in Argentina where he avereaged 10 points, 2.5 rebounds and 0.8 assists. In the 2012–13 season, he also played for Vaqueros de Bayamón, where he averaged 14.4 points, 5.6 rebounds and 3.1 assists. In the 2013–14 season, he played for the Puerto-Rican side Cangrejeros de Santurce, where he averaged 9.8 points, 2.2 rebounds and 0.9 assists. In the 2014–15 season at Cangrejeros de Santurce, he averaged 12.5 points, 2.3 rebounds and 1.2 assists in that season. In the 2015–16 season, he continued playing at Cangrejeros de Santurce, he averaged 10.5 points, 2.7 rebounds and 1 assists in that season. In the 2016–17 season, he moved to the Puerto-rican side Piratas de Quebradillas, where he averaged 8.2 points, 2.6 rebounds and 2.5 assists. He moved back to Vaqueros de Bayamón in the 2017–18 season, in that season, where he averaged 13.8 points, 4.9 rebounds and 3.0 assists. In the 2018–19 season at Vaqueros de Bayamón, Mojica averaged 18.8 points, 3.6 rebounds and 3.4 assists.
International career
Mojica represented the Puerto Rican Basketball National team at the 2008 FIBA World Olympic Qualifying Tournament for Men in Athens Greece, where he averaged 3 points, 3.6 rebounds and 0.2 assists during the tournament. Javier Mojica also represented the Puerto Rican Basketball National team at the 2019 FIBA Basketball World Cup where he averaged 2 points and 1.8 rebounds and 0.2 assists.