The date was 1986, known as the "merger year", when two schools - May River Academy and Sea Pines Academy - became Hilton Head Preparatory School. But the story doesn't start in 1986; the story of Hilton Head Prep begins much earlier encompassing students, teachers, and campuses in both Bluffton and at the back door of Sea Pines Plantation.

In 1965, Sea Pines Academy (SPA) was founded as an independent, non-profit educational institution. The history of Sea Pines Academy is rooted in the man many consider as the "founder" of Hilton Head Island itself: the late Charles Fraser. As the early development of the Island blossomed in the mid-sixties, the Sea Pines Company and Fraser approached the Beaufort County schools system about establishing a south-end school. Because Fraser's company was appealing to prospective residents and management employees, a solid school became a top priority. In 1965, the Sea Pines Company shouldered 80% of the costs to start a private school for local children in first through seventh grades. SPA’s colors were green and yellow and their mascot was the Gator.

By 1972, the school expanded, offering first through twelfth grades. Also during 1972, SPA moved to its 15-acre campus two blocks from the ocean, adjacent to the Sea Pines Forest Preserve. This tract of land is the current home of Hilton Head Preparatory School.

In 1971, May River Academy (MRA) opened its doors to a class of first grade students on its Bluffton campus. MRA's mascot was the Patriot and the school colors were red and columbia blue.

By 1985, SPA had to face fiscal reality. Enrollment had topped out at 240 students, and the future looked uncertain. MRA was experiencing its own struggles keeping its doors open.

In an attempt to revitalize the two fledgling schools, the Marathon Oil Company, developer of Port Royal, Indigo Run, Shipyard, and Wexford Plantations on the Island proposed the merger of May River Academy and Sea Pines Academy, creating a single, stronger school. The oil company offered to provide land within the Indigo Run complex. Plans called for both MRA and SPA to eventually sell both campuses, merge into the new Indigo Run campus, pay off all debt, and boast an enrollment of some 500 students.

However, the economy faltered and so did some of the plans for the merger. Both the MRA and SPA campuses continued to exist until a physical merger occurred during the 1985-86 school year incorporating the grounds of SPA. The new school, Hilton Head Preparatory School, was deeded ten acres in Sea Pines Plantation. By selling the MRA campus in 1988 Hilton Head Prep was able to pay down some of its lingering debt. Eventually, Hilton Head Prep sold back some of the Sea Pines land to reduce its long-term debt.

Hilton Head Prep joined the National Association of Independent Schools in the 90’s and has grown and flourished through outstanding leadership, strong and dedicated faculty and loyal students, families and alumni. In 2005, Hilton Head Prep celebrated its 40th birthday with much celebration and the kick-off of its first-ever major capital campaign. Following the lead of hard working volunteers who raised almost $1,000,000 to build the KNS Media Center in 1990, Hilton Head Prep’s “Tradition of Excellence” capital campaign raised more than $6,500,000 to build the Joseph B. Fraser, Jr. Field House, named in honor of Charles Fraser’s brother. Joe, who was his brother’s quiet support during the development of Hilton Head Island and who had children and grandchildren at SPA and HHP. The capital campaign also helped build an endowment fund in support of faculty development and scholarships.

Hilton Head Prep's history is one with the history of the Island itself. But despite the years and the changes they have brought, the school's mission has never wavered. Hilton Head Prep seeks to educate college-bound students in a safe environment. Instilling personal integrity is central to our educational purpose. We strive to prepare a diverse population of qualified students for academic challenges, for a successful college experience, and for rewarding lives.