We report a 14-year-old girl in whom a diagnosis of primary central nervous system lymphoma was confirmed while receiving growth hormone (GH) for GH deficiency, detected after presenting with short stature. MRI revealed an enhancing and thickened pituitary stalk with absence of the normal bright signal in the posterior pituitary. Regular MRI surveillance detected progression of the neurohypophyseal changes 13 months into GH treatment. Biopsy confirmed this to be B-cell large cell lymphoma. This case highlights the diagnostic and management challenges inherent in treating such children.