Background To describe the complications and long-term results in patients with multiple endocrine neoplasia type 2A (MEN 2A) syndrome in whom a prophylactic thyroidectomy was performed, in relation to the recommendations of the American Thyroid Association (ATA). Methods A retrospective study of 14 patients with MEN 2A thyroidectomized between 2000 and 2017. We reviewed demographic, clinical, analytical and radiological data. Postoperative complications and long-term follow-up were analyzed. Results We treated eight boys and six girls with a median age of 5 years old (range 2–10). The predominant genetic mutation belonged to codon 634 (8/14, 57.14%). Total thyroidectomy (TT) without cervical lymphadenectomy was performed in all patients. A right upper parathyroidectomy was performed in one patient due to intraoperative suspicion of increased volume. Histological study revealed no alterations. Two patients presented transient hypocalcemia postoperatively and no patient had permanent hypocalcemia or nerve damage. Pathological anatomy confirmed medullary thyroid microcarcinoma in 5/14 patients: all carrying codon 634 mutation and three of them with preoperative basal calcitonin levels <20 pg/mL. No recurrences or metastases have been detected after a mean follow-up of 8 years. A patient with codon 634 mutation developed a unilateral pheochromocytoma at 25 years of age. No patient has presented hyperparathyroidism. Conclusions Prophylactic thyroidectomy without cervical lymphadenectomy is an effective and safe preventive treatment in patients with MEN 2A syndrome when it is performed by experienced surgeons in reference centers.