Background: Tailgut cysts are rare congenital lesions that develop in the presacral space. As they can potentially conceal primary neuroendocrine tumors, surgical excision is suggested as the treatment of choice. However, specific management guidelines have yet to be developed. A posterior approach is usually preferred for cysts extending to the third sacral vertebral body. Conversely, a transabdominal approach is preferred for lesions extending upward to achieve an optimal view of the surgical field and avoid injuries. Case report: Here, we report a case of a 48-year-old man suffering from perianal pain and constipation. Digital rectal examination and magnetic resonance imaging revealed a presacral mass below the third sacral vertebral body. A laparoscopic transabdominal presacral tumor excision was performed. The final histological diagnosis was a rare primary neuroendocrine tumor arising from a tailgut cyst. The postoperative course was uneventful, and no signs of recurrence were observed at the six-month follow-up. Conclusions: This study may help establish more well-grounded recommendations for the surgical management of rectal tumors, demonstrating that the laparoscopic transabdominal technique is safe and feasible, even for lesions below the third sacral vertebral body. This approach provided an adequate view of the presacral space, facilitating the preservation of cyst integrity, which is essential in cases of malignant pathologies.