Trigeminal neuralgia (TN) is a severe facial pain disorder characterized by brief, electric shock-like pain triggered by innocuous stimuli, commonly affecting middle-aged women. TN can be classified as classic, secondary, or idiopathic, with the secondary form linked to multiple sclerosis (MS). Treatment typically begins with carbamazepine or oxcarbazepine, but surgical and alternative treatments, including botulinum toxin type A (BoNT-A), may be considered for refractory cases. We present the case of a 47-year-old female with secondary progressive MS and refractory TN, initially diagnosed in 2008. Following a history of failed pharmacological and surgical interventions, including microvascular decompression and gamma knife surgery, the patient was admitted to a rehabilitation center for motor, cognitive, and functional recovery. Her severe pain, which did not respond to conventional medication, impaired her participation in rehabilitation, leading to the use of BoNT-A as a new intervention. A total of 100U of BoNT-A was injected subcutaneously across the most painful facial regions, at 1 cm intervals. Following the BoNT-A injection, the patient reported a marked reduction in pain (VAS score reduced from 8-9/10 to 1/10), less frequent exacerbations, and reduced dependence on emergency analgesics. The only adverse effect observed was transient ipsilateral facial paresis (House-Brackmann grade II). This case underscores the potential of BoNT-A as a valuable adjunctive therapy for TN, particularly in complex patients where traditional medical and surgical options have failed. BoNT-A was well-tolerated, providing substantial pain relief with minimal side effects. Despite the absence of standardized guidelines for its use in TN, this case supports its consideration in refractory cases, highlighting the need for further research to optimize dosing and administration techniques.