Child growth and development are important aspects of the quality of human capital in future. This study aimed to examine the association between stunting and fine motor, gross motor, and social independence development among children under the age of five years old. We included a total of 525 children from district level survey in Sedayu Subdistrict, Yogyakarta, Indonesia, for further analysis. Stunting was associated with fine motor (OR = 3.45; 95% CI: 1.22–9.76) and social independence (OR = 7.09; 95% CI: 2.01–25.01), but not gross motor skill (OR = 2.43; 95% CI: 0.67–8.81). Performance ratios of fine motor (p = 0.02) and social independence (p = 0.01) skills were also higher among non-stunted children compared to stunted children.