As a significant piscivorous predator, the pikeperch (Sander lucioperca) plays a critical role in regulating aquatic ecosystems. Understanding its size-related feeding behaviour is thus vital for assessing its impact. To evaluate its role in the ecosystem, stomach content analysis provides useful insights into predator–prey dynamics. This study investigated the stomach content and dietary patterns of pikeperch in the Lipno Reservoir, Czech Republic, across two distinct time periods: the 1966–1970 (19’s) and the 2010–2022 (20’s). We analysed the stomach contents of 875 pikeperch specimens and revealed a notable shift in diet composition over time. The results demonstrated a significant decrease in overall prey consumption and a marked increase in the proportion of cyprinids in the diet, whereas the percentages of perch (Perca fluviatilis) and ruffe (Gymnocephalus cernua) decreased. Cannibalism was observed in the 20’s dataset, suggesting a reduction in prey abundance in the reservoir or a shift in community structure. The predator–prey length ratio (PPR) decreased as pikeperch grew larger. The PPR values in Lipno Reservoir were lower than those reported in other studies, indicating potentially slower growth rates in this fish. Although percids were the main prey of pikeperch, the electivity index showed positive values only for pikeperch as the prey. Overall, this study highlights long-term changes in pikeperch diets, both in the numbers and species of prey and in PPR.