Acene molecular crystals are of current interest in organic optoelectronics, both as active materials and for exploring and understanding new phenomena. Phonon scattering can be an important facilitator and dissipation mechanism in charge separation and carrier transport processes. Here, we carry out density functional theory (DFT) calculations of the structure and the full phonon dispersion of crystalline naphthalene, a well-characterized acene crystal for which detailed neutron diffraction measurements, as well as infrared and Raman spectroscopy, are available. We evaluate the performance, relative to experiments, of the local density approximation (LDA); the generalized gradient approximation of Perdew, Burke, and Ernzerhof (PBE); and a recent van der Waalscorrected non-local correlation functional (vdW-DF-cx). We find that the vdW-DF-cx functional accurately predicts lattice parameters of naphthalene within 1%. Intermolecular and intramolecular phonon frequencies across the Brillouin zone are reproduced within 7.8% and 1%, respectively. As expected, LDA (PBE) underestimates (overestimates) the lattice parameters and overestimates (underestimates) phonon frequencies, demonstrating their shortcomings for predictive calculations of weakly-bound materials. Additionally, if the unit cell is fixed to the experimental lattice parameters, PBE is shown to lead to improved phonon frequencies. Our study provides a detailed understanding of the phonon spectrum of naphthalene, and highlights the importance of including van der Waals dispersion interactions in predictive calculations of lattice parameters and phonon frequencies of molecular crystals and related organic materials.