Joseph Friedrich Nicolaus Bornmüller (February 6, 1862 – December 19, 1948) was a German botanist who was born in Hildburghausen, Thuringia.
He studied horticulture in Potsdam, and in 1886 travelled to the Balkans and Greece on his first botanical expedition. In 1887-88 he worked at the Botanical Garden in Belgrade, and during his subsequent career performed botanical studies widely throughout the Middle East, Asia Minor and southern Europe. In 1903 he succeeded Heinrich Carl Haussknecht (1838–1903) as curator of the "Haussknecht Herbarium" at Weimar, a position he maintained until 1938. He was also awarded an honorary professorship from the University of Jena.
Among Bornmüller's many publications was a treatise on Macedonian flora titled Beiträge zur Flora Mazedoniens (1925–1928). The plant genus Bornmuellerantha from the family Scrophulariaceae is named in his honor.