The usual dietary intake of vitamin D was studied in 10 subgroups of the Czech population. Food consumption data was collected using repeated 24 h recall in a national cross-sectional survey (the Study of Individual Food Consumption, SISP04), and the vitamin D content in marketed foods was quantified within the national Total Diet Study (2014–2015). The Monte Carlo Risk Assessment computational model (version MCRA 8.2) was used to assess usual intake. The median vitamin D intakes for the Czech population (aged 4–90 years, both genders) were within a range of 2.5–5.1 μg/day. The highest median intake, excluding dietary supplements, was observed in men aged 18–64, and the lowest was observed in children aged 4–6 and girls aged 11–17. The main sources in the diet were hen eggs (21–28% of usual dietary intake), fine bakery wares (11–19%), cow’s milk and dairy products (7–23%), meat and meat products (4–12%), fish (6–20%), and margarines (7–18%). The dietary intake of vitamin D for more than 95% of the Czech population was below the recommended Dietary Reference Values (DRVs). These findings should encourage public health authorities to support interventions and education and implement new regulatory measures for improving intake.