Although neurological features are commonly encountered in Whipple’s disease (WD), presentation with purely neurologic patterns is uncommon. Exclusive confinement to the central nervous system (CNS) is extremely rare. In these cases, the development of isolated cerebral mass is exceptional. In the present paper, the authors describe a case of a 68-year-old man who presented with partial seizures. The neurological examination was normal. The imaging showed a cystic lesion. This tumor-like lesion was removed by performing frontal craniotomy. A histopathological investigation revealed the presence of numerous perivascular foamy histiocytes infiltrating the brain parenchyma. The majority of these histiocytes harbored PAS-positive intense staining ,which is distinctive feature of cerebral WD. The diagnosis was confirmed by PCR analysis of cerebrospinal fluid. There were no gastrointestinal symptoms and no PAS inclusions in intestinal mucosa. The patient received Ceftriaxone intravenously followed by oral trimethoprime-sulfamethoxazol (TMP-SMZ) for 12 months and recovered well. This case illustrates atypical WD, confined exclusively to the central nervous system.