High-yielding cultivars with high water use efficiency are a main target in maize breeding; yet, no comprehensive study about the genetic regulation of photosynthesis, or about the ranges of variability for gas exchange-related parameters in maize has been published. Here, a large maize panel of 731 inbred lines previously genotyped was evaluated to elucidate the genetic basis of photosynthesis-related parameters, measured 15–30 days after silking, across three years. Large phenotypic and genotypic variations were observed in this panel with dramatic fluctuations in heritability for various traits. We detected 27 minor Quantitative Trait Loci (QTL), comprising 39 significant trait-Single Nucleotide Polymorphisms (SNPs), located mostly on chromosomes 5 and 8. Most candidates genes were novel, though a few of them were functionally associated with the theory of source-to-sink translocation presented in previous studies. Genomic selection of favorable alleles to enhance photosynthesis, along with other tools, could be a practical, and a promising, approach in the future. Leaf net photosynthesis and stomatal conductance are the most promising targets for breeding programs. We did not find any marker associated with intrinsic water use efficiency, which highlights that developing maize cultivars with more efficient use of water by genomic selection is not straightforward; however, given the high heritability value for this trait, phenotypic selection could be implemented.