Joel Asaph Allen (July 19, 1838 - August 29, 1921) was an American zoologist and ornithologist.

He studied at Harvard University under Louis Agassiz. He participated in one expedition to Brazil and in several others within the United States. In 1873 he was the head of the naturalists of the North Pacific Railroad expedition from Bismarck, North Dakota to the Yellowstone and back for the Smithsonian.

Allen was the first curator of birds and mammals at the American Museum of Natural History (from 1885 on) and later the first head of its Department of Ornithology.

In 1886, he was one of the incorporators of the first Audubon Society, New York.