Local food prices are key indicators of food security and market conditions. Yet price data are often not available, particularly for rural areas of Sub-Saharan Africa. We compiled data from 168 markets to study spatial and temporal price variation. We found that prices slightly increase when the preceding growing season was dry. Across the continent, there is pronounced seasonal variation, with lowest prices 2–3 months after harvest and highest prices just before harvest. A predictive model explained 42% of the spatial variation in prices. Our results show that spatial and temporal price variation can be generalized and that prices can be estimated for unsampled locations or months. Such estimates may be used to improve the targeting of food security interventions and strengthen empirical policy-oriented research.