The current case study evaluated the effect of vital pulp therapy on a human dental pulp after a long-term period using micro-computed tomography (MCT) for the first time. In the presented report, the successful outcomes of full pulpotomy using calcium-enriched mixture (CEM) cement on an irreversible pulpitis case were documented clinically/radiographically over 5 years. Due to an unrestorable crown fracture at the 5-year recall, the tooth was extracted and evaluated by MCT; the images showed that CEM pulpotomy allowed the dental pulp to create complete dentinal bridges without pulp canal obliteration (PCO). These MCT results showed that CEM pulpotomy, as a bio-regenerative treatment, caused no negative consequence of PCO or calcific metamorphosis on dental pulp over the long term.