Having chosen the medical profession, he rapidly attained an eminent position.
He acquired a large fortune, and gave so liberally to his two nephews that one, Sir Alexander Wedderburn, acquired the estate of Blackness, while the other, Sir Peter Wedderburn, bought Gosford House in East Lothian in 1659.
At Gosford, Sir John lived in partial retirement from 1662 till his death in July 1679, and was probably buried in the churchyard of Aberlady.
By his will he bequeathed his extensive and valuable library to St. Leonard's College, St. Andrews University.
A portrait of him was in the possession of Sir William Wedderburn, at Meredith, England.