The aim of the study was to present rarely reported neurologic complications in Nijmegen breakage syndrome. A 13-year-old female was referred because of chronic progressive headaches. There were dysmorphic features on physical examination, which suggested a diagnosis of chromosomal instability syndrome. The results of genetic and immunologic examinations confirmed the diagnosis. Cerebral magnetic resonance imaging revealed an 8 mm thickening of the meninges over the left hemisphere, corresponding with a chronic inflammatory condition, and symptoms of left cavernous thrombophlebitis were detected. Cerebrospinal fluid examination and an infusion test demonstrated disorders in its absorption. Antibiotic, anticoagulant and cerebral edema treatment was given and after 1 week improvement was observed. Regression of symptoms occurred after 14 days.