The modern institution originated as a 1985 union of previously independent upper and lower schools.

The lower dates to 1894, originally based at Park Road in central Douglas.

A review of secondary education in Douglas in 1985 formed St. Ninians, establishing a new name and uniting the two parts.

While primarily aimed at supporting primary schools, the computer bus facilitated a trip to London for St. Ninian's students in 1999.

The new lower school in Onchan has several tennis courts, playing fields, modern football pitches and a large gymnasium.