Purpose: To report a rare case of congenital bilateral vitreous cysts associated with a unilateral cataract in a pediatric patient and describe the clinical, surgical, and histopathologic findings. Methods: A single pediatric case was reviewed. Results: A 5-year-old boy with no significant past medical history presented after a failed vision screening, with symptoms of light sensitivity and frequent rubbing of the left eye. Examination revealed bilateral vitreous cysts and a unilateral cataract. The cyst in the left eye with the cataract was large and obscured the macula. The patient underwent pars plana vitrectomy and lensectomy. Postoperatively, optic nerve head and macular swelling with retinal dragging were observed, possibly owing to the mechanical effect of the cyst. Intraoperatively, the cyst was found to have attachments to the temporal pars plana, with adjacent chorioretinal scars in both eyes. Histopathologic analysis demonstrated cuboidal and spindle cells consistent with a diagnosis of a primary non-pigmented ciliary body epithelial cyst. Evaluation for acquired etiologies was unremarkable. Conclusions: This case highlights a rare presentation of congenital vitreous cysts with associated cataract and retinal structural changes. Histopathologic findings supported a primary non-pigmented ciliary body epithelial origin after exclusion of acquired causes.