Reducing sodium (Na) intake is an urgent global challenge, especially in East Asia and high-income Asia-Pacific regions. However, the sources of Na and their effects on urinary Na excretion have not been fully studied. We sought to clarify these sources and their association with urinary Na excretion. We examined four 3-day weighed food records and five 24-h urinary collections from each of 253 participants in Japan, aged 35–80 years, between 2012 and 2013. We compared the levels of Na according to four categories: foods contributing to discretionary or nondiscretionary Na intake, the situation in which dishes were cooked and consumed, food groups and types of cuisine. We also conducted regression analysis in which 24-h urinary Na excretion was a dependent variable and the amounts of food intake in the four categories were independent variables. Levels of Na were the highest in discretionary intake (60.6%) and in home-prepared dishes (84.0%). Of the food groups, miso soup showed the highest percentage contribution to Na intake (13.3%) after seasonings such as soy sauce. In the regression analysis, the standardised coefficient for foods of nondiscretionary Na sources was larger than that for discretionary sources, whereas that for home-prepared dishes was consistent with the levels of Na in those foods. Pickled products, followed by fresh fish and shellfish, miso soup and rice, were associated with high urinary Na excretion. Thus, discretionary foods (such as miso soup) contribute the most to Na consumption, although nondiscretionary intake (such as pickled vegetables) may influence urinary Na excretion.