Trejo took Cruz Azul to the Copa Libertadores de América final against Boca Juniors in 2001, which made Cruz Azul the first Mexico team to reach the Libertadores final. The game ended 1–1 on aggregate, and had to be determined on penalties.
In 2006, Trejo won the Clausura with Pachuca.
One day after he won the league, Trejo signed with Tigres to be their coach for one year. Despite having a good record for the first few games, the team began showing lack of commitment. Soon, the record showed eight consecutive games without winning, including a 7–0 defeat against Toluca, and all the responsibility was put on Trejo's management. His last game with Tigres was against Pachuca, the very same team he had made champion a year before. After the team lost 5–0, he was fired on 1 October 2006. Trejo was not unemployed for long, as he was hired by Necaxa after manager Hugo Sánchez left to coach the Mexico national team.
On 4 September 2013, Trejo became the new manager of UNAM.
[3] On August 15, 2014, after UNAM suffered their 4th consecutive loss, Trejo was sacked and David Patiño was named interim coach.[4]
