We aimed to determine the usual intake of total fat, fatty acids (FAs), and their main food sources in a representative cohort of the Spanish pediatric population aged 1 to <10 years (n = 707) who consumed all types of milk and an age-matched cohort who consumed adapted milk over the last year (including follow-on formula, toddler’s milk, growing-up milk, and fortified and enriched milks) (n = 741) who were participants in the EsNuPI study (in English, Nutritional Study in the Spanish Pediatric Population). Dietary intake, measured through two 24 h dietary recalls, was compared to the European Food Safety Authority (EFSA) and the Food and Agriculture Organization of the United Nations (UN-FAO) recommendations. Both cohorts showed a high intake of saturated fatty acids (SFAs), according to FAO recommendations, as there are no numerical recommendations for SFAs at EFSA. Also, low intake of essential fatty acids (EFAs; linoleic acid (LA) and α-linolenic acid (ALA)) and long-chain polyunsaturated fatty acids (LC-PUFA) of the n-3 series, mainly docosahexaenoic acid (DHA) were observed according to EFSA and FAO recommendations. The three main sources of total fat and different FAs were milk and dairy products, oils and fats, and meat and meat products. The consumption of adapted milk was one of the main factors associated with better adherence to the nutritional recommendations of total fat, SFAs, EFAs, PUFAs; and resulted as the main factor associated with better adherence to n-3 fatty acids intake recommendations. Knowledge of the dietary intake and food sources of total fat and FAs in children could help in designing and promoting effective and practical age-targeted guidelines to promote the consumption of EFA- and n-3 PUFA-rich foods in this stage of life.