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Rice (Oryza spp.) is the major staple food for most countries in West Africa, but local production does not meet demand. Rice is grown mainly by smallholder farmers, and yields are generally low with high temporal and spatial variability. Low yields have been attributed to unfavorable climate conditions, poor soil quality, and sub-optimum agricultural practices. The objectives of this study were to assess variation in yields of three major rice production systems (irrigated lowland, rainfed lowland, and upland) across three climatic zones (semi-arid, sub-humid, and humid), and identify factors affecting that variation. We analyzed data on yield, climate, soil, and agricultural practices for 1305 farmers’ fields at 22 sites in 11 West African countries between 2012 and 2014. A boundary function approach was used to determine attainable yields. Random forest algorithm was used to identify factors responsible for yield variation. Average rice yield was 4.1, 2.0, and 1.5 t ha(-1) in irrigated lowland, rainfed lowland, and rainfed upland systems, respectively, with maximum attainable yields of 8.3, 6.5, and 4.0 t ha(-1). Yield difference between attainable and average yield tended to be higher in irrigated and rainfed lowland systems. In those two systems, yields were highest in the semi-arid zone, while no difference in yields among climatic zones was apparent for upland rice. High rice yields were associated with high solar radiation, high