Purpose: This study attempted gaining insight into the intake of protein and fat of 12- to 36-month-old children in the Netherlands. Methods: In 2017, a Total Diet Study (TDS) was carried out in the Netherlands including following three age groups: 12–17-, 18–23- and 24- to 36-month-old children. Protein and fat concentrations of 164 composite samples were analysed and combined with the consumption data from the Dutch National Food Consumption Survey 2012–2016 (DNFCS). Results: Median protein intake of the 12- to 35-month-old Dutch children based on the TDS was 35 g/day with main contributions from the food subgroups “milk and milk-based beverages”, “beef” and “yoghurts and desserts”. Median fat intake was 34 g/day with main contributions from the food subgroups “margarines”, “cheeses” and “milk and milk-based beverages”. For the youngest age group (12- to 18-month-old children), (ready to drink) follow-on formula was one of the main contributors to the fat intake. Conclusion: Compared to the EFSA reference values, protein intake of the Dutch 12- to 36-month-old children is high, whereas fat intake follows the reference intake. A TDS is a suitable instrument to estimate macronutrient intakes.