Anhui University of Chinese Medicine was founded in 1959; its predecessor was the Anhui Provincial TCM Training Class established in 1952. In 1959, the Anhui provincial government officially approved the establishment of Anhui College of Traditional Chinese Medicine. In 1970, the college merged into Anhui Medical College. In 1975, the Ministry of Education approved its restoration. In 2000, Anhui Medical School merged in. In 2011, the provincial government approved establishing the Anhui Academy of Chinese Medicine Sciences on its basis. In 2013, the Ministry of Education approved renaming it Anhui University of Chinese Medicine.

The university is a national TCM clinical research base, a national TCM international cooperation base and a national drug clinical research base, authorized to confer doctoral degrees and recommend master's students without entrance exams. It has four campuses—Shaoquan Lake, Meishan Road, Shihe Road and Lu'an Road—with 18,194 full-time students (including 2,673 doctoral and master's students), 17 secondary colleges and departments (including 3 directly affiliated hospitals) and 7 non-directly affiliated hospitals.