Bannayan-Riley-Ruvalcaba syndrome (BRRS) is characterized by macrocephaly, pigmented macules on the glans penis and benign mesodermal hamartomas. 9.6-year-old boy was referred to the pediatric surgeon following an observation of a subcutaneous lipomatous lesion and numerous nodules in the thyroid gland via ultrasonography performed due to swelling in the neck first noticed approximately 3 months previously. Thyroid ultrasonography revealed numerous nodules with distinct margins in both lobes of the thyroid gland, some exhibiting calcification and others hypoechoic areas, and a total thyroidectomy was performed due to a suspicion of malignity. After surgery, the patient was referred to the Pediatric Endocrinology Department. On physical examination, his weight was 30 kg [standard deviation score (SDS): -0.38], height 140 cm (SDS: 0.71) and head circumference 59.5 cm (SDS: +3.21). Pubic hair was Tanner stage 2, bilateral testes 3+3 mL palpable. There was multiple hyperpigmented lesions on the penile skin. His past medical history revealed that pubic hair development was reported at the age of 8 years. Laboratory examinations revealed a 17-OH progesterone level of 4.8 ng/mL, bone age compatible with 8 years. P.V281L heterozygous mutation was determined via CYP21A2 mutation screening performed for non-classic congenital adrenal hyperplasia. BRRS was primarily suspected in this case of macrocephaly, lipomatous lesions and pigmented macular lesions on the penis. Heterozygous p.C136R mutation was determined via PTEN mutation scanning.