Marker-assisted breeding could significantly increase progress in improving crop drought tolerance, if QTL with significant effects on crop yield in stress environments can be identified. The objective of this research was to obtain a first assessment of a putative drought tolerance QTL on linkage group 2 (LG 2) of pearl millet. This was done by comparing hybrids made with topcross pollinators (TCP) based on progenies selected from the original mapping population for presence of the tolerant allele at the target QTL versus field performance in the phenotyping environments. A set of 36 topcross hybrids was evaluated in 21 field environments, which included both non-stressed and drought-stressed treatments during the flowering and grain filling stages. The QTL-based hybrids were significantly, but modestly, higher yielding in a series of both absolute and partial terminal stress environments. However, this gain under stress was achieved at the cost of a lower yield in the non-stressed evaluation environments. This particular pattern of adaptation in the QTL-based hybrids was consistent with their general phenotype—early flowering, limited effective basal tillering, low biomass and a high harvest index (HI)—which resembled that of the drought tolerant parent of the original mapping population. The results thus confirmed the effectiveness of the putative drought tolerance QTL on LG 2, but suggested that it may enhance drought tolerance by favoring a particultar phenotype with adaptation to terminal stress.