How does the brain represent musical properties? Even with our growing understanding of the cognitive neuroscience of music, the answer to this question remains unclear. One method for conceiving possible representations is to use artificial neural networks, which can provide biologically plausible models of cognition. One could train networks to solve musical problems, and then study how these networks encode musical properties. However, researchers rarely examine network structure in detail because networks are difficult to interpret, and because many assume that networks capture informal or subsymbolic properties. Here we report very high correlations between network connection weights and discrete Fourier phase spaces used to represent musical sets. This is remarkable because there is no clear mathematical relationship between network learning rules and discrete Fourier analysis. That networks discover Fourier phase spaces indicates that these spaces have an important role to play outside of formal music theory. Finding phase spaces in networks raises the strong possibility that Fourier components are possible codes for musical cognition.