The Wilkinson School was founded in 1977 by Linda Wilkinson with just six students. Ed and Linda Wilkinson expanded in 1980 from a one site serving grades K-6 to include a licensed children's center for thirty-six preschool-aged children in Moss Beach and a middle school for grades 6-8 in Half Moon Bay.

In 2009, the school was purchased by Timothy Miller, who had just completed his third year with the school as principal, and Doug Bannick, a parent and long-time supporter of the school. Under their leadership, the Wilkinson School continues to offer an elementary education which balances the highest quality academics, enrichment through empirical studies, the arts, and nurturing in small classes with highly-qualified teachers.