In this case report, we described the pitfalls in the differential diagnosis of a pituitary stalk lesion in a patient affected by Klinefelter Syndrome (KS) that was initially suspected of infundibulo-neuro-hypophysitis (INH). According to the atypical radiological picture for INH, the not-conclusive pathology findings, and the partial response to glucocorticoid treatment, a [18F] fluorocholine ([18F] FCH) positron emission computed tomography (PET-CT) scan was performed and identified a pituitary stalk proliferative lesion that was suggestive for neoplasia. This clinical case emphasizes the prospective and potential diagnostic role of the [18F] FCH PET-CT in pituitary stalk lesions and in the diagnosis of pituitary germinoma. Our article also includes a brief review of the literature, focusing on the differential diagnosis of lesions involving the pituitary stalk, the oncological risk associated with KS, and the role of nuclear imaging in the evaluation of such cases.