Whipple disease (WD) is a rare systemic disorder caused by the bacteria Tropheryma whipplei. In its classic form, it manifests with gastrointestinal problems including diarrhea, abdominal pain, and weight loss. However, various other systems can be affected, including the central nervous system (CNS). Even more rarely, the CNS is primarily affected without gastrointestinal symptoms and with a negative small bowel biopsy. The incidence of primary CNS WD is unknown. We report the case of a young female with the primary CNS form of WD. In this report, we highlight the main clinical features and diagnostic procedures that lead to the diagnosis and comment on the treatment and clinical response. We stress the importance of neuroimaging and brain biopsy. A unique feature of this case is that the patient has been followed up for 12 years. At the time of diagnosis, no neurological manifestations were detected, although a tumor-like lesion in the right temporal lobe and hypothalamic infiltration were present on magnetic resonance imaging (MRI). The first neurological manifestations developed 2 years later despite recommended antibiotic treatment, with cognitive impairment developing more than 10 years later. According to the MRI findings and clinical course, the disease was active for several years when multiple lesions on MRI appeared despite antibiotic therapy. In the discussion, we compare the present case with similar cases previously reported and we elaborate on the similarities and discrepancies in clinical features, diagnostic procedures, results, and treatment options.