John Hodges Allen founded Allen Academy in 1886. Allen is one of the oldest independent schools in the state of Texas. Originally located in Madisonville, the school moved in 1889 to the nearby town of Bryan and in 1988 settled to its current location. The campus is located in an area enjoying significant residential and business growth and has ample room for the school's long-term plans and development. In addition to the physical plant, a rapidly growing community has bolstered current enrollment and is indicative of the need for a challenging, college preparatory school in the community.

As an independent school, Allen is governed by a self-perpetuating Board of Trustees. The Board is responsible for setting institutional policy, hiring and evaluating the Head of School, and ensuring the school's financial health and security. The Board entrusts the daily operations of the School to the Head of School, who supervises and evaluates all programs and personnel, and is the final arbiter of any disputes that may arise.

Allen's Board is comprised of nine trustees. An Executive Committee of four members leads the Board and its four standing committees - the Audit Committee, the Development Committee, the Finance Committee, and the Governance Committee. Members serve in three-year terms.

Bob Meyer is the Head of School at Allen. He is supported by an administrative team of directors to include:

• Assistant Head of School - Caren Walton
• Director of Admissions and Marketing – Layne Neuenfeldt
• Business Manager - Jeff Fountain