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BACKGROUND AND OBJECTIVES: Trigeminal neuralgia (TN) is a headache characterized by paroxysmal episodes of intense pain in the facial region. TN can occur secondary to structural mechanisms, such as vascular compression of the trigeminal nerve root. Basilar invagination (BI) is a malformation of the craniovertebral junction characterized by invagination of the odontoid process of the axis through the foramen magnum into the posterior fossa, and 1% of cases may present associated TN. This article presents a clinical case of TN secondary to BI and vascular compression of the trigeminal nerve root, which responded only to treatment with botulinum toxin type A. CASE REPORT: A 34-year-old patient with a clinical presentation consistent with TN for approximately 12 years. The symptoms were debilitating and impacted the quality of life, culminating in constant insomnia, severe depression, and suicidal thoughts. Treatment with botulinum toxin type A was fundamental in managing this patient’s pain. CONCLUSION: The case reported here demonstrated the therapeutic success of treatment with botulinum toxin type A in a complex and refractory case of pain syndrome.