Few studies have assessed the association between sodium (Na) and potassium (K) and migraine headaches. In this study, we aimed to examine the relationship between 24-hour urine Na and K intakes and clinical findings of migraine in an Iranian sample. In this cross-sectional study, 262 participants, aged 20–50 years, were included with a body mass index (BMI) of 18·5–30 kg/m2 and a diagnosis of migraine. One 24-hour urine sample was collected from each subject to estimate the Na and K intakes. The clinical features of migraine, including frequency, duration, severity, Migraine Headache Index Score (MHIS), and Headache Impact Test (HIT) score, were assessed. Besides, a multiple linear regression analysis was performed, and beta estimates and the corresponding 95% confidence intervals (CIs) were reported. Overall, 224 women and 38 men, with a mean age of 36·10 years and BMI of 25·55 kg/m2 comprised our study population. After controlling for potential confounders, the 24-hour urine Na was positively associated with a longer headache duration (β = 0·29; 95% CI: 0·06, 0·53) in the group with the highest urine Na levels as compared to the group with the lowest levels. After adjustments for potential confounders, an increase of 13·05 in the MHIS was observed when the 24-hour urine Na level increased from the first to the third tertile (β = 13·05; 95% CI: 1·70, 24·41). Our findings suggested that a higher 24-hour urine Na level was positively associated with a longer duration of migraine headaches and a higher MHIS.