To determine the association between women’s autonomy and the presence of childhood anemia in children under five years of age in Peru, a cross-sectional study utilizing data from the 2019 Demographic and Family Health Survey was carried out. The study employed generalized linear models with a Poisson distribution and log link function. Crude and adjusted prevalence ratios (aPR) were calculated, along with their corresponding 95% confidence intervals (CI), to assess the association of interest. A total of 15,815 women and their children under five years of age were analyzed. The prevalence of childhood anemia was 30.4% (95%CI: 29.5–31.3%), while the proportions of low, moderate and high autonomy of the mothers were 44.5%, 38.4% and 17.1%, respectively. Children under five years of age of women with a low level of autonomy were more likely to have anemia (aPR: 1.10; 95%CI: 1.00–1.21). Three out of ten children under five years of age suffer from anemia, and four out of ten mothers have a low level of autonomy. A low level of women’s autonomy was associated with a higher probability of anemia in children under 5 years of age.