Abstract Pikeperch Sander lucioperca is a cool-water fish considered to be a potential aquaculture species. At present, extreme temperature conditions in summer affect the growth and survival of pikeperch cultured in ponds, indicating that the effects of heat stress on pikeperch merits research attention. In this study, pikeperch were heat stressed at 29 °C for up to 48 h. Fish were sampled at different time periods, and changes in gills histopathology and oxidative stress status were determined. The gill transcriptome under heat stress and significantly differentially expressed genes were also analyzed. qPCR was used to detect the expression of antioxidant-related genes and Hsp member family genes in gills of fish subjected to different durations of heat stress. The degree of gill damage increased with prolongation of the heat stress. The activities of total superoxide dismutase (T-SOD), glutathione peroxidase (GPx), catalase (CAT) and glutathione reductase (GR) and the malondialdehyde (MDA) content in the gills changed significantly in response to continued heat stress. The expression of 252 genes changed significantly under heat stress: 191 genes were up-regulated and 61 genes were down-regulated. KEGG pathway enrichment analysis showed that multiple pathways were involved in the heat-stress response of the pikeperch but mostly involved lipid metabolism (six pathways), followed by amino acid metabolism (four pathways), carbohydrate metabolism (three pathways), and folding, sorting and degradation. The expression of antioxidant-related genes, including Cu Zn SOD, Mn SOD and CAT, and the heat shock protein (Hsp) member family genes increased during the early period of heat stress, but decreased in the later period. The overall results indicate that the gills of pikeperch are sensitive to heat stress and pikeperch actively responds to heat stress through regulating the antioxidant system, and the expression of Hsp genes and genes involved in energy metabolism. This study improves our understanding of the effects of heat stress on pikeperch, and reveals the mechanism of the heat-stress response in this species.