We discuss and analyze the virtual element method on general polygonal meshes for the time-dependent Poisson-Nernst-Planck (PNP) equations, which are a nonlinear coupled system widely used in semiconductors and ion channels. After presenting the semi-discrete scheme, the optimal $H^1$ norm error estimates are presented for the time-dependent PNP equations, which are based on some error estimates of a virtual element energy projection. The Gummel iteration is used to decouple and linearize the PNP equations and the error analysis is also given for the iteration of fully discrete virtual element approximation. The numerical experiment on different polygonal meshes verifies the theoretical convergence results and shows the efficiency of the virtual element method.