Purpose: We present the case of a 4-month-old boy with a large orbital cyst that caused lateral displacement of the optic nerve resulting in progressive exophthalmos of the left eye since birth.Case summary: A 4-month-old boy presented with progressive exophthalmos of the left eye since birth. Physical examination revealed marked left eye proptosis. Magnetic resonance imaging revealed microphthalmia and a 2.2 × 1.9 cm orbital cyst in the retrobulbar region. Subsequently, an anterior orbitotomy of the left eye was performed to dissect and excise the cyst. Histopathological examination revealed an orbital cyst containing neuroectodermal tissue. No complications or recurrences were observed during the 3-month post-surgery period.Conclusions: Congenital microphthalmia with orbital cysts is a rare condition that does not always require surgical intervention. However, timely surgical intervention in cases of severe exophthalmos can result in favorable functional and cosmetic outcomes. We present a case that exhibited significant improvement following surgical removal of the orbital cyst.