Objective To anatomically reconstruct the oculomotor nerve, trochlear nerve, and abducent nerve by skull base surgery. Methods Seventeen cranial nerves (three oculomotor nerves, eight trochlear nerves and six abducent nerves) were injured and anatomically reconstructed in thirteen skull base operations during a period from 1994 to 2000. Repair techniques included end-to-end neurosuture or fibrin glue adhesion, graft neurosuture or fibrin glue adhesion. The relationships between repair techniques and functional recovery and the related factors were analyzed.Results Functional recovery began from 3 to 8 months after surgery. During a follow-up period of 4 months to 6 years, complete recovery of function was observed in 6 trochlear nerves (75%) and 4 abducent nerves (67%), while partial functional recovery was observed in the other cranial nerves including 2 trochlear nerves, 2 abducent nerves, and 3 oculomotor nerves.Conclusions Complete or partial functional recovery could be expected after anatomical neurotization of an injured oculomotor, trochlear or abducent nerve. Our study demonstrated that, in terms of functional recovery, trochlear and abducent nerves are more responsive than oculomotor nerves, and that end-to-end reconstruction is more efficient than graft reconstruction. These results encourage us to perform reconstruction for a separated cranial nerve as often as possible during skull base surgery.