Rhabdomyosarcoma (RMS) is a common soft tissue malignancy of the pediatric age group, frequently involving the head and neck region; however, nasopharyngeal RMS is a rare entity. By virtue of its parameningeal involvement and nonspecific presentations, nasopharyngeal RMS has become a clinical challenge to diagnose. We present a case of an eight-year-old boy presenting with signs and symptoms of nasal obstruction who was initially being treated for tonsillitis. Recurrent episodes led to detailed examination and radiologic imaging, and a diagnosis of Thornwaldt cyst was made. For the relief of symptoms, a debulking surgery was performed followed by a biopsy which revealed the mass to be a nasopharyngeal RMS. Our case highlights the importance of including nasopharyngeal RMS into the differentials of midline nasal masses along with the role of biopsy for confirming its diagnosis as treatment modalities for it are strikingly different than the other more common group of conditions, i.e., benign nasal masses. While surgery is usually delayed in the latter group, it can be of prime importance while treating nasal RMS, along with chemotherapy and radiotherapy.