The club participated in the Apertura and Clausura tournaments of the Mexican Primera División and in the 2003 Copa Libertadores.
UNAM had a good first semester, classifying to the playoffs as the third best team from the regular season.
In the playoffs, the defeated Cruz Azul in the quarterfinals but were eliminated by Morelia at the semifinals.
After winning the Pre Libertadores mini tournament, the team made its presentation in the continental tournament losing 2–3 against Grêmio on their first match, but managed to advance to the round of 16, being eliminated by Chilean side Cobreloa.
In 2002 UNAM participated in the Pre Libertadores trying to earn a spot in the 2003 edition of the tournament.