Research examining radiation damage and its effects in graphite began in the 1940’s during the development of moderated nuclear reactors. Interest in this topic is expanding because of emerging applications associated with fullerenes and carbon nanostructures as well as its long-standing use as a fission moderator. In this work, we report the measurements of the full phonon density of states of irradiated nuclear graphite using inelastic neutron scattering experiments at room temperature. The samples were previously exposed to different levels of neutron doses and irradiation temperatures. The phonon density of states of perfect and defected graphite supercells including different configurations of vacancies and interstitials were calculated using first-principles direct method. Despite high neutron irradiation doses, the scattering measurements show that the induced damage is localized, and the layered structure is preserved. A comparison of the measured phonon densities of states of irradiated samples with those calculated of defected supercells indicates that the main changes observed are mainly attributed to formation of vacancies.