Objectives: Cone-beam CT (CBCT), a radiographic tool for diagnosis, treatment, and follow-up in dental practice, was introduced also in pediatric radiology, especially orthodontics. Such patients subjected to repetitive X-rays examinations may receive substantial levels of radiation doses. Ionizing radiation (IR), a recognized carcinogenic factor causing DNA double-strand breaks (DSBs) could be harmful to undifferentiated cells such as dental pulp stem cells (DPSCs) since inaccurately repaired or unrepaired DSBs may lead to malignant transformation. The H2AX and MRE11 proteins generated following DSBs formation and pro-inflammatory cytokines (CKs) secreted after irradiation are relevant candidates to monitor the cellular responses induced by CBCT. Methods: DPSCs were extracted from human exfoliated deciduous teeth and their phenotype was assessed by immunocytochemistry and flow-cytometry. Cells were exposed to IR doses: 5.4–107.7 mGy, corresponding to 0.5–8 consecutive skull exposures, respectively. H2AX and MRE11 were detected in whole cells, while IL-1α, IL-6, IL-8, TNFα in supernatants, using enzyme-linked immunosorbent assay (ELISA) at different time points after exposure. Results: The phosphorylation level of H2AX in DPSCs increased considerably at 0.5 h after exposure (p <0.001 for 3, 5, 8 skull exposures and p <0.05 for 1 skull exposure, respectively). MRE11 response could only be detected for the highest IR dose (p <0.001) in the same interval. CKs secretion increased upon CBCT exposure according to doses and time. Conclusions: The DPSCs exposure to CBCT induces transient DNA damage and persistent inflammatory reaction in DPSCs drawing the attention on the potential risks of IR exposures and on the importance of dose monitoring in pediatric population.