This clinical report describes the implementation of magnetic resonance imaging (MRI) to evaluate a patient with long-standing velopharyngeal dysfunction. She was referred to the craniofacial clinic at age 10 with no prior surgical history and subsequently completed a Furlow palatoplasty due to a suspected submucous cleft palate. However, results were unfavorable with minimal improvement in speech or resonance. The clinical presentation, treatment, outcomes, and contributions from MRI for secondary surgical planning are described. Addition of MRI into the clinical workflow provided insights into the anatomy and physiology of the velopharyngeal mechanism that were unable to be obtained from nasendoscopy and speech evaluation alone.