Recently, over-parameterized neural networks have been extensively analyzed in the literature. However, the previous studies cannot satisfactorily explain why fully trained neural networks are successful in practice. In this paper, we present a new theoretical framework for analyzing over-parameterized neural networks which we call neural feature repopulation. Our analysis can satisfactorily explain the empirical success of two level neural networks that are trained by standard learning algorithms. Our key theoretical result is that in the limit of infinite number of hidden neurons, over-parameterized two-level neural networks trained via the standard (noisy) gradient descent learns a well-defined feature distribution (population), and the limiting feature distribution is nearly optimal for the underlying learning task under certain conditions. Empirical studies confirm that predictions of our theory are consistent with the results observed in real practice.