He was the son of Stephen Mackenzie. He married Margaret Bouch.
He was physician in the London Hospital from 1866 to 1873. He was the founder of the Hospital for Diseases of the Throat (1863). He was the first Englishman to become expert in operations on the larynx and adjacent parts. He was for some time the physician to Emperor Frederick III of Germany. For his services there, he was awarded a knighthood in 1887. AMW's son, William McNeill Whistler worked with Mackenzie at the Hospital for Diseases of the Throat.