Klinefelter syndrome (KS) is the most common chromosomal aneuploidy in male population, which demonstrates an unusual association with acromegaly. We herein present a rare case involving the confirmation of KS 2 years after surgical treatment for acromegaly. A 27-year-old man presented with an acromegalic appearance. Endocrinological examination revealed a high growth hormone (GH) concentration, low testosterone concentration, and high follicle-stimulating hormone and luteinizing hormone concentration. Brain imaging revealed a 9 x 6 x 7-mm sellar low-density nodule suggestive of a microadenoma. Trans-sphenoidal surgery was undertaken, and immunohistochemistry revealed GH positivity. Two years after surgery, the patient underwent examination for infertility. He presented with diminished pubic hair, and small and firm testes. Hormonal assay revealed hypergonadotrophic hypogonadism on the basis of decreased serum total testosterone (<0.2 ng/mL), and elevated luteinizing hormone (14.71 mIU/mL) and follicle-stimulating hormone (21.8 mIU/mL). A chromosomal karyotype examination showed 47, XXY, confirming the diagnosis of KS. Replacement therapy with oral testosterone undecanoate was begun. Brain imaging showed no delayed enhancement in the saddle region of the pituitary gland, but the concentration of plasma insulin-like growth factor maintained a high level. The patient's GH concentration was not significantly suppressed by the GH glucose suppression test. In this consideration, he was referred for postoperative somatostatin analogue treatment to control GH hypersecretion. The misdiagnosis or delayed diagnosis of KS is mainly because of substantial variations in clinical presentation and insufficient professional awareness of the syndrome itself. As the simultaneous occurrence of KS and acromegaly is rare, and the association between them remains unclear, we suggest that complete pituitary hormonal screening and conventional pituitary MRI should be essential for patients with KS to screen for pituitary tumor.