Background: Chronic malnutrition in children is a severe global health concern. In Yogyakarta, the number of children who are too short for their age has dropped dramatically over the past few decades. Objective: To perform an analysis of trends, policies, and programs; and an assessment of government, community, household, and individual drivers of the stunting reduction in Yogyakarta, Indonesia. Method: Using a mixed-methods approach, there were three types of research: (1) analysis of quantitative data, (2) evaluation of stunting policy, and (3) focus group discussions and in-depth interviews to collect qualitative data. Results: The prevalence of stunting has decreased from year to year. Mean height-for-age z-scores (HAZ) improved by 0.22 SDs from 2013 to 2021. Male and female toddlers aged <20 months have relatively the same body length as the WHO median, but it is lower for children >20 months old. The COVID-19 pandemic has contributed to an increase in stunting-concurrent wasting. Nutrition-specific and -sensitive interventions have been carried out with coverage that continues to increase from year to year, although in 2020, or at the beginning of the COVID-19 pandemic, the coverage of specific interventions decreased. The government has committed to tackling stunting by implementing the five pillars of stunting prevention and the eight convergent stunting actions. As the drivers of stunting reduction, national and community stakeholders and mothers, at the village level, cited a combination of poverty reduction, years of formal education, prevention of early marriage, access to food, enhanced knowledge and perception, and increased access to sanitation and hygiene. Conclusions: Nutrition-specific and -sensitive sector improvements have been crucial for decreasing stunting in Yogyakarta, particularly in the areas of poverty reduction, food access, preventing child marriage, sanitation, education, and increasing knowledge and perception.