Pleural effusion is a rare complication of ventriculoperitoneal (VP) shunting, usually due to the migration of the VP shunt catheter into the thorax. Herein we report a neurologically disadvantaged child with a lobar holoprosencephaly and hydrocephalus, initially treated with a VP shunt, who years later developed recurrent right-sided pleural effusion ultimately confirmed to be a cerebrospinal fluid (CSF) hydrothorax without intra-thoracic migration of the distal shunt catheter. Thoracentesis was compatible with a transudative effusion. Given the presence of a persistent pleural effusion, beta-2 transferrin concentrations were measured, which yielded a positive result. Plain radiographs and head computed tomography (CT) showed a normally positioned, functional VP shunt. A spine CT myelogram to look for a spinal dural-thoracic CSF fistula was negative. A radionuclide CSF shunt study demonstrated normal functioning VP shunt with radiotracer accumulation within the peritoneum, with subsequent tracer rapidly accumulating in the right hemithorax. Video-assisted thoracoscopic (VATS) exploration with drainage of the pleural effusion and pleurodesis was then performed. No diaphragmatic defect or shunt tubing within the thorax was found and the procedure failed to resolve the effusion. The patient's recurrent effusion was ultimately resolved with intracranial endoscopic choroid plexus coagulation to decrease CSF output.