He was a student at the universities of Munich and Jena, earning his doctorate at the latter institution in 1884. In 1887 he obtained his habilitation, becoming a professor of phylogeny at Jena two years later. From 1898 he served as professor of comparative anatomy and zoology at the University of Breslau and director of the zoological museum. In 1918 he was appointed professor of zoology at the University of Berlin as well as director of the zoological museum. In 1918-19 he was president of the German Zoological Society.
In 1886 and 1889 Kükenthal traveled to regions in the Arctic, and in 1893-94, with support from the Senckenberg Natural History Society, participated in an expedition to Borneo and the Moluccas. He specialized in the study of Octocorallia, a taxonomic subclass that includes sea pens, sea fans and soft corals. He also conducted embryological and comparative anatomical investigations of whales and other marine mammals. His large collection of zoological specimens is now housed at the Senckenberg Museum in Frankfurt.
He has over twenty zoological species named after him, including Calamorhabdium kuekenthali (Batjan iridescent snake), Emoia kuekenthali (Kuekenthal's emo skink), Hemirhamphodon kuekenthali (Kuekenthal's halfbeak), Parantica kuekenthali (Kuekenthal's yellow tiger), and Lysmata kuekenthali (Kuekenthal's cleaner shrimp).
- Vergleichend-anatomische und entwickelungsgeschichtliche Untersuchungen an Walthieren, (1889)
- Forschungsreise in den Molukken und in Borneo : im Auftrage der Senckenbergischen naturforschenden Gesellschaft (1896) - Expedition to the Moluccas and Borneo, on behalf of the Senckenberg Natural History Society.
- Leitfaden für das Zoologische Praktikum (1898) - Manual of practical zoology.
- Australien, Ozeanien und Polarländer (1902, 1910; with Wilhelm Sievers in Sievers’ Allgemeinen Länderkunde) - Australia, Oceania and Polar Lands.
- Pennatularia (1915)
- Gorgonaria (1919).
- Deutsche Biographie (biography of Willy Georg Kükenthal)
- Parts of this article are based on a translation of an equivalent article at the German Wikipedia.