[3] After a summer program testing teaching concepts and forming the first group of students, the school opened in fall 2000 with 102 9th-grade students,[4][5] split between two sites in downtown San Jose, near the San Jose State University campus: St. Paul's Methodist church (in 2007 the site of the launch of a charter elementary school, Rocketship One)[2] and a YWCA.

[10] Initial plans of constructing a school building on land donated by San Jose State fell through.

[15][16][17][18] The building was gutted to create a "great area" and other new spaces; Downtown College Prep students and their math teacher assisted the architect, Bill Gould, in laying out the partitions for the interior rebuilding.

[19] Gould had been the designer with Glen Rogers of the Spirit Gate, a San Jose Public Art Program project completed in 2000 consisting of an ornamental gateway on The Alameda with concrete posts resembling elephant tusks and inspirational "power words" such as "family" and "dream" stencilled out of the circular gate itself.

[22][23] In 2008, Downtown College Prep opened an affiliated middle school (6th–8th grade) in Alviso, in North San Jose.