Kükenthal was born to August Kükenthal (1826-1910) and Minna Wimmer (died 1917) and went to school at Weißenfels and Halle before joining the University of Munich where he studied mineralogy and later zoology at Jena, earning his doctorate at the latter institution in 1884 for studying lymphoid cells in annelids.

He travelled around the North Sea with B. Weißenborn and joined the zoology department Jena under Ernst Haeckel in 1885.

In 1886, with support from the Senckenberg Natural History Society, he participated in an expedition to Borneo and the Moluccas.

From 1898 he served as professor of comparative anatomy and zoology at the University of Breslau (Wrocław) and as director of the zoological museum which in the present day is the Museum of Natural History, University of Wrocław ("Muzeum Przyrodnicze Uniwersytetu Wrocławskiego" in Polish).

He published the Leitfaden für das Zoologische Praktikum (1898) and from 1913 he edited along with Thilo Krumbach the Handbuch der Zoologie.