Leaf size is a major determinant of plant architecture and yield potential in crops. A population consisting of 244 backcross recombinant inbred lines derived from the cross of 93-11 and ZS97, both elite indica hybrid rice parents, were developed for quantitative trait loci (QTL) detection. Seven pleiotropic QTL regions are detected affecting leaf size (i.e. flag leaf length, width) and yield traits (i.e. panicle weight and panicle length) simultaneously. Among of them, the QTL (qFL1) was shown to explain a large proportion of the variation in flag leaf size in the derived backcross-populations in multiple environments. qFL1 had a pleiotropic effect on flag leaf size and yield-related traits. Using a large segregating population, we narrowed the location of qFL1 to a 31 kb region containing four predicted genes. Expression of one of these genes, OsFTL1, differed between leaves in the near-isogenic lines carrying alleles of ZS97 and 93-11. Pyramiding of qFL1 with two known genes (gs3 and wx) from 93-11 into ZS97 could enlarge flag leaves, improve grain size and amylose content, and also increase yield per plant, but slightly delayed heading date. These results provide a foundation for the functional characterization of the gene underlying the pleiotropic effects of qFL1 and for genetic improvement of the plant architecture and yield potential of rice.