St. Anne School was founded as a Christian School in accordance with the Roman Catholic tradition in 1992 by a group of parents, clergy and community leaders serving children of all faiths in Pre-School through 7th grade.

The original site was a leased parcel of land in Laguna Niguel situated with modulated classrooms. Throughout the next three years St. Anne School experienced steady enrollment, and during the 1995 school year a committee of parents located and arranged for the purchase of 7.5 acres of land in Laguna Niguel for the permanent home of St. Anne School.

Phase I opened on September 12, 1996. On September 14, 1998, Phase II, a 25,000 square foot multi-purpose building opened. This facility, called the Queen of Life Center, includes classrooms, a gymnasium, chapel, kitchen, stage, locker rooms, and offices. On September 15, 1999, Phase III, named Christ the King was occupied by the kindergarten through fourth grade students. The administrative offices and conference rooms are also a part of Phase III. The final phase, Mother Theresa Center, opened in March, 2000. Mother Theresa Center houses the Pre-School, Daycare Center, Library, Middle School, and specialty classrooms Art and Music. Now complete, St. Anne School's 95,000 square foot facility accommodates over 800 students in Pre-School through eighth grade.

St. Anne School is a California non-profit religious corporation, registered as a tax-exempt organization with the federal and state authorities under Internal Revenue Code Section 501(c)(3) and is eligible to accept tax deductible donations. It does not discriminate on the basis of race, religion, national or ethnic origin.