Sterol carrier protein-2 (SCP-2) is an intracellular, small, basic protein domain that in vitro enhances the transfer of lipids between membranes. It is expressed in bacteria, archaea, and eukaryotes. There are five human genes, HSD17B4, SCPX, HSDL2 STOML1, and C20orf79, which encode SCP-2. HSD17B4, SCPX, HSDL2, and STOML1 encode fusion proteins with SCP-2 downstream of another protein domain, whereas C20orf79 encodes an unfused SCP-2. We have extracted SCP-2 domains from databases and analyzed the evolution of the eukaryotic SCP-2. We show that SCPX and HSDL2 are present in most animals from Cnidaria to Chordata. STOML1 are present in nematodes and more advanced animals. HSD17B4 which encodes a D-bifunctional protein (DBP) with domains for D-3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase, and SCP-2 are found in animals from insects to mammals and also in fungi. Nematodes, amoebas, ciliates, apicomplexans, and oomycetes express an alternative DBP with the SCP-2 domain directly connected to the D-3-hydroxyacyl-CoA dehydrogenase. This fusion has not been retained in plant genomes, which solely express unfused SCP-2 domains. Proteins carrying unfused SCP-2 domains are also encoded in bacteria, archaea, ciliates, fungi, insects, nematodes, and vertebrates. Our results indicate that the fusion between D-3-hydroxyacyl-CoA dehydrogenase and SCP-2 was formed early during eukaryotic evolution. There have since been several gene fission events where genes encoding unfused SCP-2 domains have been formed, as well as gene fusion events placing the SCP-2 domain in novel protein domain contexts.