Pyogenic granuloma (PG) refers to a common, acquired, benign, and vascular tumor that arises in tissues such as the skin and mucous membranes. However, it is extremely rare for PG to arise from an empty socket after tooth extraction. Herein, we describe a rare case of PG that arose from the empty extraction socket of the second molar adjacent to a dentigerous cyst of the left mandibular wisdom tooth in a 57-year-old man. The patient’s second molar was extracted during the same procedure in which the wisdom tooth and cyst were removed. Subsequently, at 42 days after surgery, an exophytic mass was found in the socket of the second molar. An excisional biopsy was performed, and the histopathological diagnosis was PG. Since the PG recurred 90 days after the surgery, a complete excision with bone curettage was performed. During the 12 months of follow-up, there has been no recurrence observed. In conclusion, as tooth extraction is a routine dental practice, clinicians should be aware that PGs can also develop from an extraction socket.