The escalating extreme weather conditions has forced rural farmers in Africa to rely disproportionately on Indigenous Fruit Trees (IFTs) to sustain their household food/nutrition security, employment and income generation. This paper analysed farmers’ use of IFTs to cope with climate variability in selected Lake Victoria Basin Districts of Uganda. Data were collected from farmers using questionnaires, key informant interviews and focus group discussions. From 13 most preferred IFTs, focus was on the most popular and highly ranked five: Garcinia buchananii, Vangueria apiculata, Canarium schweinfurthii, Tamarindus indica and Saba comorensis. Preferences for these IFTs were influenced by their uses for food, medicine, timber, compound shade provision and marketability. Age, sex, education, occupation, family size, land size, non-farming activities, period of stay on the same piece of land, and income level significantly (P≤0.05) influenced choice of the preferred IFTs. Majority of the respondents had IFTs planted on-farms, along the roads to provide various goods/services and in marginal lands unsuitable for farming to diversify agriculture as a strategy to cope with climate variability. Given that the uses of IFTs in the five LVB districts are associated with farmers’ efforts to cope with climate variability, the goal of any climate-adaptive farmer-based project should support sustainable use of IFTs, in the short-term and foster innovations such as on-farm planting of IFTs and other fast-growing tree species to meet household demands.