The question of how musical training can influence perceptual and cognitive abilities of children has been the subject of numerous past studies. However, evidence showing which neural mechanisms underlie changes in cognitive skills in another domain following musical training has remained sparse. Syntax processing in language and music has been shown to rely on overlapping neural resources, and this study compared the neural correlates of language- and music-syntactic processing between children with and without long-term musical training. Musically trained children had larger amplitudes of the ERAN (early right anterior negativity), elicited by music-syntactic irregularities. Furthermore, the ELAN (early left anterior negativity), a neurophysiological marker of syntax processing in language, was more strongly developed in these children, and they furthermore had an enlarged amplitude of a later negativity, assumed to reflect more sustained syntax processing. Thus, our data suggest that the neurophysiological mechanisms underlying syntax processing in music and language are developed earlier, and more strongly, in children with musical training.