The San Juan Knights were founded in 1999 by then-mayor and current senator Jinggoy Estrada and businessman Sandy Javier.

During the pre-season, the team acquired 6'9" Bonel Balingit from the Philippine Basketball Association to a three-year, P16 million contract.

Joining Balangit are Gherome Ejercito from the Pampanga Dragons, a cousin of Estrada, 1998 NCAA Most Valuable Player Christian Calaguio, and Chito Victolero.

In the playoffs, San Juan swept both Navotas and Quezon City, and won 2–1 against Manila to advance to the 2019 MPBL finals against the Davao Occidental Tigers.

As the playoffs began, the team swept through Pasay and Pampanga before facing the Makati Super Crunch in the North Division Finals.

The series was tied before the season's suspension but San Juan were able to win deciding game 3 against a depleted Super Crunch squad to make back-to-back National Finals appearances for a chance to repeat against the Davao Occicdental Tigers.

The rivalry between San Juan and the Davao Occidental Tigers is most prominent in the MPBL when both teams played in the National Finals in back-to-back seasons (2019 and 2021).

As of February 2024, the San Juan franchise has met the Davao Occidental Tigers a total of fifteen times across all leagues.

San Juan's rivalry against the Nueva Ecija Rice Vanguards began in FilBasket when both teams clashed in the finals of the 2022 Summer Championship.