Alternative live feeds for small and sensitive fish early life stages such as pikeperch (Sander lucioperca L., 1758) can improve the larval quantity, quality and performance in aquaculture. Therefore, this study evaluated the cyclopoid copepod Apocyclops panamensis (Marsh, 1913) as live feed for pikeperch larviculture from day 11 post hatch (dph) in two independent experiments. In both experiments, pikeperch larvae had the highest specific growth rate (SGR) when they fed on Brachionus plicatilis until dph 11 and A. panamensis until dph 16–18. SGR was related to a decrease in total fatty acids (FAs), saturated FAs and monounsaturated FAs in pikeperch larvae, indicating their use as energy for growth. Within the polyunsaturated FAs, docosahexaenoic acid (DHA) increased in larvae fed with A. panamensis and coincided with the highest SGR suggesting that DHA is accumulated in larvae as structural FA. Our study demonstrated a suitable pikeperch larval fatty acid composition for growth after feeding A. panamensis compared with Artemia sp. from dph 11 until dph 16 and previously fed with B. plicatilis. Moreover, it highlighted the importance of the dietary PUFAs in pikeperch rearing, specifically of linoleic acid (LA) from dph 4 until dph 11 and of DHA from dph 11 onwards.