The club participated in the Apertura and Clausura tournaments of the Mexican Primera División and in the 2003 Copa Libertadores.

Cruz Azul started the season under José Luis Trejo as manager, but he was sacked at the end of the Apertura tournament; club chairman Guillermo Álvarez cited the "lack of adequate results" as the main reason for firing Trejo.

[3] On 12 March 2003, in an unusual situation, chairman Guillermo Álvarez fired Mario Carrillo and the whole squad due to the bad results.

[4] Cruz Azul had not won a single match in the first nine rounds and had managed to get only six points; besides, the team had recently suffered a disgraceful 6–1 loss against Uruguayan club Fénix in the Copa Libertadores.

Despite losing on its inaugural match against Corinthians 0–1 and the 1–6 loss against Fénix, Cruz Azul advanced to the knockout stage as second best team in the group.