Heat stress during the reproductive and grain-filling stages leads to severe yield losses in rice, especially in irrigated areas during the dry season in Thailand. Thus, breeding for heat-tolerant rice is one of the strategies for developing rice crops adapted to the effects of high temperature in major growing regions. M9962, a fast neutron-induced mutant, was identified as a heat-tolerant line that was then used as a donor parent and crossed with the Phisanulok 2 (PSL2) cultivar (the recurrent parent) in a backcross breeding programme. Heat tolerance scoring under controlled greenhouse and field conditions was based on the percentage of spikelet fertility. Yield trials for the BC2F7 and BC3F6 lines were subsequently conducted under field conditions at three locations and under controlled greenhouse conditions during the dry season of 2019 (DS2019). In the early generation, 210 plants of the BC1F1 population and 440 plants of BC2F1 population were evaluated for their heat tolerance, and the spikelet fertility distribution within the BC1F1, BC2F1 and BC3F1 populations showed a skewed-right pattern. In addition, most rice plants in every generation were heat sensitive. Finally, compared with PSL2, the four-candidate heat-tolerant lines exhibited a high percentage of spikelet fertility and high yield. In addition, the one candidate line, BC2F7-6-5-4-1-1-21 was most similar to PSL2 in terms of genetic background, plant type and grain quality. Thus, backcross breeding programmes via the spikelet fertility can be used as an indirect trait to select for heat tolerance.