Post-traumatic stress disorder (PTSD) is a chronic anxiety disorder that occurs after an individual experiences a major traumatic event, characterized by the overgeneralization of fear memory, spontaneous retrieval, and impaired extinction. Recent studies have revealed that neuronal activity-induced DNA damage is not only involved in the formation and consolidation of fear memory, but also closely associated with the pathological mechanisms of PTSD due to abnormalities in its repair pathways. This review summarizes the physiological sources, molecular mechanisms, and physiological significance of neuronal DNA damage in general and the potential regulatory role of DNA double-strand breaks (DSBs) in the formation and maintenance of fear memory in particular. It also explores the underlying mechanisms by which DSBs may serve as molecular imprints of fear memory. This review also predicts the translational potential of targeting DNA damage repair pathways in PTSD treatment in the hope of providing data for developing novel therapeutic drugs for PTSD.