Following the Restoration in 1660, Scarborough was appointed physician to Charles II, who knighted him in 1669; Scarborough attended the king on his deathbed, and was later physician to James II and William and Mary. During the reign of James II, Scarborough served (from 1685-1687) as Member of Parliament for Camelford in Cornwall.
Scarborough was an original fellow of the Royal Society and a fellow of the Royal College of Physicians, author of a treatise on anatomy, Syllabus Musculorum, which was used for many years as a textbook, and a translator and commentator of the first six books of Euclid's Elements (published in 1705). He also was the subject of a poem by Abraham Cowley, An Ode to Dr Scarborough.