The presence of natal and neonatal teeth is a rare anomaly that can lead to various complications. This case report aims to highlight the potential delayed sequelae that can arise following the extraction of natal teeth. A boy aged three years and two months was referred for pain and an abscess on his lower anterior teeth. He had two natal teeth at birth, which were extracted on the second day of life due to excessive mobility and profound discomfort to the mother during breastfeeding. Surprisingly, he presented with pain in the same area where the teeth were extracted previously. Upon examination, residual root-like structures were observed at the sites of teeth 71 and 81, with an abscess noted on tooth 81. The radiographic assessment confirmed the presence of residual roots, prompting the extraction. History, clinical, radiographic, and histopathological evaluations strongly validate the diagnosis of residual natal teeth. Gentle curettage of the socket should be performed whenever possible following the extraction of natal teeth to prevent complications. Although residual tooth formation is uncommon, periodic follow-up is important to monitor for any potential problem and observe adjacent teeth eruption.