He was born at Kibworth Harcourt, Leicestershire, England, son of Dr. John Aikin, Unitarian divine, and received his elementary education at the Nonconformist academy at Warrington, where his father was a tutor. He studied medicine at the university of Edinburgh, and in London under Dr. William Hunter. He practised as a surgeon at Chester and Warrington. Finally, he went to Leiden, earned an M.D. (1780), and in 1784 established himself as a doctor in Great Yarmouth.

In 1792, one of his pamphlets having given offence, he moved to London, where he practised as a consulting physician. However, he concerned himself more with the advocacy of liberty of conscience than with his professional duties, and he began at an early period to devote himself to literary pursuits, to which his contributions were incessant. When Richard Phillips founded The Monthly Magazine in 1796, Aikin was its first editor. In conjunction with his sister, Anna Laetitia Barbauld, he published a popular series of volumes entitled Evenings at Home (6 vols., 1792—1795), for elementary family reading, which were translated into almost every European language.

In 1798 Dr. Aikin retired from professional life and devoted himself with great industry to various literary undertakings, among which his General Biography (10 vols., 1799—1815) holds a conspicuous place. Besides these, he published Biog. Memoirs of Medicine (1780), Lives of John Selden and Archbishop Usher (1812) and other works. Aside from editing The Monthly Magazine from 1796 to 1807, he conducted a paper called The Athenaeum from 1807 to 1809, when it was discontinued.

His son, Arthur Aikin, was a prominent scientist and his daughter, Lucy Aikin, was a biographer.