A summer baby, George will be one of the youngest pupils in his class when he joins Thomas's in Battersea, a school which professes a "Christian ethos".
In a statement, Kensington Palace said: "Their Royal Highnesses are delighted to have found a school where they are confident George will have a happy and confident George will have a happy and successful start to his education."
Though a Christian school, Thomas's says it is open to all faiths and school trips include visits to a local synagogue, mosque, Buddhist temple, Sikh temple and Hindu temple.
Headmaster Ben Thomas said: "We are honoured and delighted that their Royal Highnesses the Duke and Duchess of Cambridge have chosen Thomas's Battersea for Prince George.
"We greatly look forward to welcoming him and all of our new pupils to the school in September."
With 540 pupils aged between four and 13 in classes of approximately 20 each, day fees at Thomas's as £6,110, according to last year's Tatler Schools Guide.
Children are taught subjects including ballet and French from their first day.
In a welcome note to parents, headmaster Mr Thomas said: "Whilst we are proud of our record of senior school entrance and scholarship successes, we place a greater emphasis on a set of core values, which include kindness, courtesy, confidence, humility and learning to be givers, not takers."