Crocodile tears syndrome is one of the rare complications of facial paralysis. There have been several reports of cases in which botulinum toxin was found to be useful in the treatment of crocodile tears syndrome. The adverse effects, due to the paralytic action of botulinum toxin, have been reported to involve the palpebral muscle, lateral rectus and superior rectus. Therefore, we considered that it might be more appropriate to carry out the injection procedure under electromyographic guidance in order to inject botulinum toxin selectively into the lacrimal gland and protect the above-mentioned muscles. In conclusion, we recommend EMG guidance in the treatment of crocodile tears syndrome with botulinum toxin.