Fourteen years after shunt implantation, a 26-year-old patient with myelomeningocele, concomitant hydrocephalus and a ventriculoatrial cerebrospinal fluid (CSF) shunt presented with brief but recurrent episodes of fever predominantly when taking showers or during physical exertion. After 4 years of inconclusive multidisciplinary investigations, the patient progressed into end-stage renal disease before an echocardiogram revealed a vegetative plaque on the tendinous chords of the tricuspid valve. CSF cultures were grown from the shunt valve, confirming bacterial growth of Propionibacterium acnes suspected of causing subacute bacterial endocarditis and subsequent shunt nephritis. The patient was successfully treated with antibiotics combined with ventriculoatrial shunt removal and endoscopic third ventriculocisternostomy (VCS). This case illustrates the nowadays rare, but potentially severe complication of subacute bacterial endocarditis and shunt nephritis. It also exemplifies the VCS as an alternative to implanting foreign shunt systems for CSF diversion.