Enhancing photosynthesis is widely acknowledged as an underutilized strategy for increasing crop productivity. For crops like maize (Zea mays L.), even small improvements in yield can have significant implications for global food security. Although maize is a C4 species, which is considered to be more efficient than C3 photosynthesis, there is substantial evidence that there is potential for further improvement. Improving photosynthetic efficiency via targeted manipulation of non-photochemical quenching has focused on a limited set of genes that are known to be important determinants of the NPQ response in C3 plants. The C4 pathway may alter NPQ responses but only relatively few studies have explored genetic variation in NPQ kinetics in species that perform C4 photosynthesis. Here we apply high-definition phenotyping of NPQ responses and photosynthetic efficiency and quantitative trait locus (QTL) mapping using a field-grown maize Multi-parent Advanced Generation Inter-Cross (MAGIC) population, which combines the allelic diversity of eight contrasting inbred founder lines. We find substantial and consistent variation for dynamic NPQ and PSII efficiency for two consecutive field season experiments in which over 300 Recombinant Inbred Lines (RILs) were characterized. The exploration of candidate genes within three major QTL regions identified a strong impact of allelic variation in expression of the minor PSII antenna protein CP24 (LHCB6) on a major QTL for NPQ and efficiency of PSII photochemistry on chromosome 10.