The warm-season legume, cowpea (Vigna unguiculata), is an important crop that performs well in marginal environments. The effects of high temperature are among the most substantial challenges faced by growers of cowpea. Heat injury during late reproductive development sterilizes pollen such that no fruit is set. To study the inheritance of this trait and to deliver resources to breed cowpea with enhanced tolerance to heat, we performed a quantitative trait locus (QTL) analysis using 141 individuals from a recombinant inbred population made from a cross between cowpea varieties CB27 and IT82E-18. Five regions, which represent 9 % of the cowpea genome, explain 11.5–18.1 % of the phenotypic variation and are tagged with 48 transcript-derived single nucleotide polymorphism markers. Favorable haplotypes were donated by CB27 for four of these regions while IT82E-18 was the source of tolerance explained by the fifth QTL. Homeologous regions in soybean contain several genes important for tolerance to heat, including heat shock proteins, heat shock transcription factors, and proline transporters. This work presents essential information for marker-assisted breeding and supports previous findings concerning heat-induced male sterility in cowpea.