Few studies have reported association between sodium-to-potassium (Na-K) ratio and risk factors related to cardiovascular diseases (CVDs) among the general population in Asian countries. This study aimed to investigate the dietary sodium-to-potassium (Na-K) ratio association with CVD risk factors among Japanese adults. This retrospective cross-sectional study included 48,800 Japanese participants (19,386 men and 29,414 women) aged ≥20 years, registered in the 2003–2017 National Health and Nutrition Survey. Multivariate odds ratios (ORs) and 95% confidence intervals (CIs) for risk of hypertension, high glycated haemoglobin A1c (HbA1c) levels, hypercholesterolaemia, low serum levels of high-density lipoprotein (HDL) cholesterol, and high non-HDL cholesterol levels according to Na-K ratio, were estimated using logistic regression models. Dietary Na-K ratio decreased for both men and women from 2003 to 2017. Higher Na-K ratio and higher hypertension prevalence was observed (multivariate OR [fifth vs. first quintiles] = 1.27, 95% CI: 1.15, 1.40; P for trend <0.001 for men and 1.12, 95% CI: 1.01, 1.23; P for trend = 0.007 for women). Higher Na-K ratio was associated with higher prevalence of high HbA1c levels in men (multivariate OR = 1.56, 95% CI: 1.24, 1.96). Prevalence of low HDL cholesterol levels was increased with higher Na-K ratio (P for trend = 0.002 for men and <0.001 for women). No significant associations were found between Na-K ratio and hypercholesterolaemia in men or high non-HDL cholesterol levels in both men and women. Our findings suggest that dietary Na-K ratio is associated with several CVD risk factors among Japanese adults.