Run at MUCAA Leo Austria and
Dante Gonzalgo played for Lyceum while it was a member of the now defunct Manila Universities and Colleges Athletic Association (MUCAA) in the late 1970s and early 1980s.
Stint with NCRAA The Lyceum Pirates previously saw the likes of
Gary David and
Chico Lanete play for the
Intramuros-based school. Playing at the
National Capital Region Athletic Association (NCRAA), Bai Cristobal coached Lyceum at this time. The Pirates were defeated by the St. Francis Doves in the 2003 finals.
ISAA champions Coached by
Bonnie Tan starting in 2003, the Pirates won two undefeated championships in the ISAA, and two runs to the Sweet 16 in the
Philippine Collegiate Champions League (PCCL).
Entry to the NCAA Lyceum then entered the NCAA as a guest team in 2011, and was admitted as a regular member in 2015. Tan resigned as coach in 2014, and was replaced by
Topex Robinson. They would first make it to the playoffs in
2017 when
CJ Perez led them to an 18–0 elimination round record, only to lose in the finals to the
San Beda Red Lions. They would meet in an NCAA Finals rematch as a #2 seed with the Red Lions in
the next season, but still lost. The Pirates then finished second
in 2019, but lost to eventual champions
Letran Knights in the playoffs. Perlas himself didn't coach the Pirates in an NCAA game as he resigned for personal reasons in 2021; he was replaced by
Gilbert Malabanan. Malabanan coached the Pirates in the 2021 bubble season to 2–7 record, way off the play-in tournament places. The Pirates made it to the playoffs in the 2022 season, losing out to Letran in the semifinals. They made it to Final Four the following 2023 season with a twice to beat advantage as the second seed but lost both games to the eventual champions San Beda and the
Benilde Blazers in the first battle for third place in NCAA basketball history. ==Current roster==