Born to soccer columnist and former Mexico national team goalkeeper Rafael Puente, Puente Jr. began playing football as a striker with Mexican Primera División side Atlante F.C., making his professional debut in 2003.
[3] He was let go in October 2014 by newly appointed chairman Néstor de la Torre.
[6] On October 5, 2016, Puente Jr. was announced as the new manager for Ascenso MX club Lobos BUAP.
[7] On May 20, 2017, Rafael Puente Jr. successfully managed Lobos BUAP into Liga MX promotion for the 2017–18 season.
[8] On 2 April 2018, Puente Jr. was sacked after earning nine points in 13 games of the Clausura 2018 season.