Primary squamous cell carcinoma of the nasal septum is an extremely rare malignancy. In this article, we report a case of 52-year-old female with a complaint of nasal obstruction along with occasional nasal bleeding for one year. Endoscopy showed a 2.5x2 cm perforation originating from the anterior nasal septum. Incisional biopsy result was reported as squamous cell carcinoma. The tumor was removed by functional endoscopic surgery. Histopathological examination revealed squamous cell carcinoma with safe surgery borders. No recurrence and complications were noticed after one year of follow-up. The functional impact of the treatment with high mortality rates highlights the importance of early diagnosis. We recommend the differential diagnosis of septal perforation and early wide surgical excision for such cases.