This case report describes a patient with an anatomic variant of the foramen ovale that was encountered during an attempted glycerol rhizolysis for trigeminal neuralgia. Various complications have been reported during transcutaneous trigeminal neuralgia treatment. We report an adult female on whom transcutaneous cannulation of the foramen ovale was not possible. Subsequent imaging revealed a causative elongation of the spine of the sphenoid that distorted the foramen ovale and effectively blocked it. Variations in bony anatomy may complicate transcutaneous approaches to the foramen ovale for the treatment of trigeminal neuralgia.