Becoming associated with John Dalrymple, the ophthalmic surgeon, Cooper followed in his footsteps and gained a large practice.

He was one of the original staff of the North London Eye Institution, and subsequently ophthalmic surgeon to St. Mary's Hospital, Paddington.

In 1859 he was appointed surgeon-oculist in ordinary to Queen Victoria, whose sincere regard he gained (Court Circular, 2 June 1886).

It was announced on 29 May 1886 that he was to be knighted, but on the same day he was seized with acute pneumonia, of which he died on 1 June 1886. Cooper's personal character was most estimable, combining kindliness, sincerity, and simplicity with much energy.

He wrote an ‘Invalid's Guide to Madeira,’ 1840; ‘Practical Remarks on Near Sight, Aged Sight, and Impaired Vision,’ 1847, second edition 1853; ‘Observations on Conical Cornea,’ 1850; ‘On Wounds and Injuries of the Eye,’ 1859.