Introduction: Fossa navicularis magna (FNM) was defined as a notch-like defect on the inferior side of the clivus. The aim of this study was to evaluate the relationship between FNM with age and gender with cone-beam computed tomography (CBCT) in a Turkish orthodontic subpopulation. Material and Methods: The study group consisted of 195 patients (109 females and 86 males) having CBCT scans. The patients had no known syndromes, history of neurological diseases, or surgical intervention in the region of the interest. On FNM-detected patients, comparison of gender and age was performed. Descriptive statistics and Chi-square statistical analysis were made using the Statistical Package for the Social Sciences 20.0 (SPSS 20) program. P < 0.05 was accepted as statistically significant. Results: FNM was identified in 32 (17.4%) patients. Among these patients, 23 were female (21.1% of all female patients) and 9 were male (10.4% of all male patients), and the age ranged between 7 and 29 (mean age: 14 +/- 3.3) years. There was no statistically significant relationship between the presence of FNM and gender. Discussion and Conclusion: FNM is an important anatomic variation of the skull base, and it should be monitored carefully by oral and maxillofacial radiologists. The presence of fossa navicularis should also be investigated in other communities throughout CBCT, and a wider database should be established.