An apothecary in his early career, he published an essay entitled Pocket Fauna of Leipzig. Between 1863 and 1866 he worked as tradesman in Berlin and traveled through central Europe and Italy. From 1868 to 1873 he had his own factory for essential oils and attained a comfortable standard of living. Between 1874 and 1876, he traveled around the world: The Caribbean, USA, Japan, China, South East Asia, Arabian peninsula and Egypt. The journal of these travels was published as "Around the World" (1881). From 1876 to 1878 he studied Natural Science in Berlin and Leipzig and gained his doctorate in Freiburg with a monography of the genus Cinchona.
He edited the botanical collection from his world voyage encompassing 7,700 specimens in Berlin and Kew Gardens. The publication came as a shock to botany, since Kuntze had entirely revised taxonomy. His three-volume treatise, Revisio Generum Plantarum (1891) was widely rejected or deliberately ignored.
In 1886, Kuntze visited the Russian Near East and spent the 1887-1888 period on the Canary Islands. The results of both journeys became part of his main work, the Revisio. At the beginning of the 1890s he left for South America, of which he managed to see nearly all countries. In 1894, he visited the Southern African countries as well as the German colonies.
In the last years of his life, Kuntze moved permanently to Sanremo (Italy). His revolutionary ideas about botanic nomenclature created a conflict at the 2nd Congress of Botany, as a result of which the doors of the academic world were closed to him. He died in Sanremo two years later.