Pearl millet marker-assisted selection (MAS) programs targeting adaptation to variable post-flowering moisture environments would benefit from quantitative trait loci (QTLs) that improve grain yield across the full range of post-flowering moisture conditions, rather than just in drought-stressed environments. This research was undertaken to identify such QTLs from an extensive (12-environment) phenotyping data set that included both stressed and unstressed post-flowering environments. Genetic materials were test crosses of 79 F2–derived F4 progenies from a mapping population based on a widely adapted maintainer line (ICMB 841) × a post-flowering drought-tolerant maintainer (863B). Three QTLs (on linkage group [LG] 2, LG 3, and LG 4) were identifi ed as primary candidates for MAS for improved grain yield across variable post-flowering moisture environments. The QTLs on LG 2 and LG 3 (the most promising) explained a useful proportion (13–25%) of phenotypic variance for grain yield across environments. They also co-mapped with QTLs for harvest index across environments, and with QTLs for both grain number and individual grain mass under severe terminal stress. Neither had a significant QTL × environment interaction, indicating that their predicted effects should occur across a broad range of available moisture environments. We have estimated the benefits in grain yield and accompanying changes in yield components and partitioning indices that would be expected as a result of incorporating these QTLs into other genetic backgrounds by MAS.