Ernest Walton married Freda Wilson (1903–1983), daughter of an Irish Methodist minister, on 23 August 1934. They had five children, Dr Alan Walton (college lecturer in physics, Magdalene College, Cambridge), Mrs Marian Woods, Professor Philip Walton, Professor of Applied Physics, National University of Ireland, Galway, Jean Clarke and Winifred Walton. He was a longtime member of the board of governors of Wesley College, Dublin.