The present study aimed to evaluate the effect of septoplasty on the intensity and frequency of headaches in patients with deviated nasal septum attending Abu Ali Sina Regional Teaching Hospital in 1404. This descriptive-analytical study included 60 randomly selected patients. Data were collected using questionnaires that captured demographic information and assessed headache intensity and frequency. Results showed that the mean headache intensity decreased from 6.5 before surgery to 3.2 after surgery (p = 0.001). Headache frequency also reduced from 5 days per month to 1.5 days (p < 0.001). Gender-based analysis indicated that men experienced greater improvement than women, and age-based analysis revealed significant reductions in headache intensity across all age groups, although patients aged 46–65 showed relatively less improvement. These findings highlight the positive impact of septoplasty on reducing headache intensity and frequency and improving patients’ quality of life. The results of this study can contribute to the development of more effective treatment protocols and better management of symptoms in patients with a deviated nasal septum.