Size differences are common in the aquaculture of fishes. In the larviculture of cannibalistic species such as pikeperch, they majorly influence mortality rates and consequently provoke losses in the aquaculture industry. With this study, we aim to reveal molecular differences between small and large pikeperch of the same age using a set of 20 genes associated with essential developmental processes. Hereby, we applied a general study design to early and late larval pikeperch before the onset of piscivory to explore the causes of growth differences in these developmental groups. The analysis of the expression levels showed developmental but not size-related differences in PGC1A, TGFB1, MYOD1, MRF4, and the collagens COL1A1 and COL1A2. Furthermore, increased head lengths were found in larger late larvae compared to their smaller conspecifics. While no uniquely size-related expression differences were found, the expression patterns of PGC1A in combination with TGFB1 as regulators of the citric acid cycle indicate a possible influence of mitochondrial energy metabolism. Furthermore, expression differences of MYOD1 and MRF4 point out possible temporal advantages of myogenetic processes in the larger late larval group and hypothesise growth advantages of the larger late larvae resulting from various influences, which provide a promising target for future research.