Chondrosarcoma usually arises in the pelvis, ribs or long bones but rarely may occur in the nasal septum. The nasal septum chondrosarcoma may extend to skull base, paranasal sinuses or orbit which is usually observed during recurrence. Radiological examination and histopathology plays an important role for its diagnosis and to assess the grade and extension of the tumor. Moreover, the morphological differentiation of low grade chondrosarcoma from chondroma and other tumors like metastatic renal cell carcinoma, chordoma may pose diagnostic challenge on histopathology. It is therefore essential to vigilantly examine the histopathological sections for subtle features for definite diagnosis of chondrosarcoma. The present case is therefore being reported of rare tumor of low grade chondrosarcoma of nasal septum in young female extending to skull base at initial presentation. The case also highlights the importance of close histomorphological examination of low grade chondrosarcoma to avoid diagnostic pitfalls and the importance of repeat biopsy if clinico-radiological suspicion is strong and thus avoiding further complications.