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Continuum, a challenging, fast-paced performance choir, is comprised of young men ages 13 to 18 in high school with changed voices. This group is by audition and is limited to 16 voices. Continuum members read music well and often sing in four to eight parts. Many of these young men have been singing with the Pacific Boychoir Academy for five to 10 years, though some come from other choir backgrounds as well. Members of the Changed Voices choir are former Troubador or Trouvere members whose voices have changed. They typically are between the ages of 13 and 18.

The Trouvere choir is a subset of the Cantori choir. This elite subset is comprised of boys ages 10 to 14, and their goal is to be one of the best after school boys choirs in America. These choristers learn a more sophisticated repertoire and occasionally sing with the Troubadors. They have performed with the San Francisco Symphony and at events around the Bay Area, in addition to performing and touring with Cantori.

The Cantori choir is a performance choir comprised of boys roughly ages 8 to 11. These choristers often have the opportunity to travel around the Bay Area and the United States to give performances. Their rehearsals are repertoire-intensive, where they sing in two to three parts and continue more advanced music-reading techniques. Cantori have toured Arizona, Southern California, the Pacific Northwest, Canada, and Hawaii.

The Intermezzi choir is comprised of boys who have been promoted from Minstrels or who have some musical experience, ages eight and nine. In Intermezzi, choristers start to focus on repertoire and singing in parts. The director works with them on singing vowels and consonants. The Intermezzi music theory work consists of rhythm and solfege (Do-Re-Mi) work with the aim of having choristers read notes in a piece of music and not just words.

The Minstrels are the youngest and most inexperienced choristers of the Pacific Boychoir Academy, typically ages six and seven. Minstrels begin their PBA experience by learning all about music and teamwork. They work with Orff instruments to internalize beats and familiarize themselves with rhythmic patterns. Their music theory work focuses on the basics of music reading and singing, the different kinds of notes, how to breathe properly, etc.

Prelude is the Pacific Boychoir's early childhood music program designed to help children gain confidence in their singing abilities and musical talents. This unique program aims to establish fundamental music skills to prepare children for the next step in their musical life.

Ensembles include the Youth Jazz Orchestra; Jazz Comobs; Latin Salsa Band; OPC Symphony Orchestra; Zimbabwe Marimba Band; Symphonic Wind Ensemble; Count Basie Tribute Orchestra, Shekere Ensemble, and the Frederick Douglass Youth Ensemble.

I am Me uses the music of Branice McKenzie to teach life lessons. Through singing music from South African Township to Big Band Swing, children learn about friendship, community, listening, family, gratitude, manners, and much more through play, movement, and song.