Saint Paul's School takes great pride in its independent school status. The term “independent” refers to schools that are members of the National Association of Independent Schools (NAIS). Such a membership means non-profit, governed by a board of trustees, independent of control by any government or church agency, and therefore, not a parochial school. Members of NAIS are non-discriminatory regarding race, religion, or ethnic origin in the hiring of faculty and staff, admission of students, and administration programs.

The NAIS membership is a privilege granted only to those private schools meeting specific standards of governance and operation. NAIS schools carry accreditation from regional accrediting organizations. Saint Paul's School is fully accredited by the Florida Council of Independent Schools, the Florida Kindergarten Council and the Southern Association of Colleges and Schools (SACS). To maintain these important memberships, accredited schools must undergo rigorous evaluation. The FCIS evaluation occurs every five years and results in the school following prescribed principles of good practice.

NAIS schools seek excellence in a variety of ways: they provide small classes, excellent teaching, and academic programs appropriate to the school’s mission. It is the belief and desire of Saint Paul's School that every student can and should excel within this framework.

Saint Paul's School is also a member of other professional organizations. The Bay Area Association of Independent Schools (B.A.A.I.S.), the National Association of Episcopal Schools (E.A.E.S.), the Council for American Private Education (C.A.P.E.), Council for Spiritual and Ethical Education (C.S.E.E.), Independent School Management (I.S.M.), Independent Educational Services (I.E.S.), Educational records Bureau (E.R.B.), Association for Supervision and Curriculum Development (A.S.C.D.). and Elementary Schools Heads Association (E.S.H.A.).