The presence of two phenotypes in a single species is a widespread phenomenon, also observed in European eel (Anguilla anguilla). This dimorphism has been related to dietary differences in the subadult elver and yellow eel stages, with broad-heads generally feeding on harder and/or larger-bodied prey items than narrow-heads. Nevertheless, both broad- and narrow-headed phenotypes can already be found among glass eels, the stage preceding the elver eel stage. As these glass eels are considered nonfeeding, we investigate here to what degree the observed variation in head width is reflected in variation in the musculoskeletal feeding system, as well as whether this reflects the same variation observed in the older, dimorphic yellow eels. Additionally, we investigate whether musculoskeletal differences between broad- and narrow-headed glass eels have implications on their feeding performance and could thus impact prey preference when eels start feeding. Therefore, we compared the cranial musculoskeletal system of five broad- and narrow-headed glass eels using 3D-reconstructions and simulated the glass eel's bite force using the data of the muscle reconstructions. We found that the variation in the musculoskeletal system of glass eels indeed reflects that of the yellow eels. Broader heads were related to larger jaw muscles, responsible for mouth closure. Accordingly, broad-heads could generate higher bite forces than narrow-headed glass eels. In addition, broader heads were associated with higher coronoid processes and shorter hyomandibulae, beneficial for dealing with higher mechanical loadings and consequently, harder prey. We, thus, show that head width variation in glass eels is related to musculoskeletal differences which, in turn, can affect feeding performance. As such, differences in prey preference can already take place the moment the eels start feeding, potentially leading to the dimorphism observed in the elver and yellow eel stage.