A molecular understanding of the proteins involved in fructose metabolism is essential for controlling the current spread of fructose‐related obesity, diabetes and related adverse metabolic states in Western populations. Fructose catabolism starts with the phosphorylation of d‐fructose to fructose 1‐phosphate by ketohexokinase (KHK). KHK exists in two alternatively spliced isoforms: the hepatic and intestinal isoform KHK‐C and the peripheral isoform KHK‐A. Here, the structure of apo murine KHK (mKHK), which differs from structures of human KHK in overall conformation, is reported. An isoform‐selective ligand, which offers a 50‐fold higher potency on mKHK and human KHK‐A compared with KHK‐C, is further characterized. In mKHK, large‐scale conformational changes are observed upon ligand binding. The structures suggest a combined strategy for the design of species‐ and isoform‐selective KHK inhibitors. [ABSTRACT FROM AUTHOR]