There is limited evidence regarding the possible role of dietary acid load (DAL) in the pathophysiology of migraine headaches. Therefore, we sought to examine DAL in relation to the clinical features of migraine including headache frequency, severity and duration, headache impact test-6 (HIT-6), and serum levels of nitric oxide (NO). In the present cross-sectional study, 262 patients (38 men and 224 women aged 20–50 years) were recruited through a simple random sampling method. Dietary intakes were obtained by using a validated 168-item semi-quantitative food frequency questionnaire (FFQ). DAL was then calculated by two different methods; potential renal acid load (PRAL) and net endogenous acid production (NEAP). In total, 262 patients with a mean (SE) age of 36.1 (0.53) and a BMI of 25.55 (0.21) were included in the current study. After controlling for potential confounders, a higher DAL was positively associated with headache frequency in those with the highest DAL score compared to the lowest (PRAL; β = 2.33; 95% CI 0.78, 3.88; NEAP; β = 1.74; 95% CI 0.13, 3.34). Increasing NEAP from 28.96 to 35.89 resulted in a 3.43 and 2.74 increment in HIT-6 scores in the crude (95% CI 1.35, 5.52) and fully-adjusted models (95% CI 0.40, 5.07), respectively. Moreover, a higher dietary PRAL was significantly associated with migraine-related disability, as shown by HIT-6, in subjects of the third tertile compared to those in the first tertile after controlling for confounders (β = 2.42; 95% CI 0.13, 4.70). In conclusion, our study highlighted the importance of the acid–base properties of a diet in the pathophysiology of migraine headaches. However, further well-designed studies are needed to confirm our findings.