Isolated third nerve palsy develops in numerous intracranial pathologies such as closed head trauma, tumor, and aneurysm. Isolated oculomotor nerve palsy caused by shrapnel injury is uncommon. After a penetrating intracranial shrapnel injury, our patient with oculomotor ophthalmoplegia underwent surgery. Microsurgery removed the shrapnel that was applying pressure on the third nerve, resulting in contusion. A partial recovery associated with regeneration was observed at month 9. Extraocular muscle surgery should be planned if palsy does not resolve over a prolonged period of time.