A 47-year-old male presented with abducens nerve palsy due to basilar impression associated with atlanto-occipital assimilation manifesting as slowly progressive bilateral trigeminal neuralgia and diplopia in the right lateral gaze. X-ray and computed tomography of the skull confirmed the diagnosis of basilar impression and atlanto-occipital assimilation, and magnetic resonance imaging disclosed tightness of the posterior cranial fossa. Surgical suboccipital decompression resulted in gradual resolution of the patient's complaints, and no additional symptoms were recognized. Impairment of the sixth cranial nerve is a rare symptom compared to those of the fifth or the eighth cranial nerve in a patient with a craniocervical malformation. However, the present case shows the possibility of cranial nerve dysfunction due to tightness of the posterior cranial fossa, and suggests that surgical treatment for basilar impression with atlanto-occipital assimilation should be considered in patients with uncommon and unusual symptoms.