Functionalist anthropology has a contested legacy. Some scholars have praised functionalism as a contributor to the relativizing of civilizations and cultures while others have criticized it as a colonial science smoothing the interwar workings of indirect rule. This article argues that the colonial politics of functionalist anthropology can only be understood against the background of resurgent settler colonialism in British East Africa. Supporters of indirect rule increasingly relied on a language of scientific administration and welfarist policies associated with the League of Nations to bolster their position against the settlers in the 1920s and 1930s. Functionalism offered them some means of support on this count. The functionalists, meanwhile, co-opted the language of indirect rule to pursue their own intra-disciplinary ends. This combination of interests was pragmatic and flexible rather than ossified and ideological, marked more by what both opposed (settler colonialism) than a shared ideal towards which they aspired (indirect rule). Anthropologists and colonial administrators possessed very different ideas of indirect rule, with strikingly different implications for the future of Britain's African Empire.