The COVID-19 pandemic revealed the need to reconsider the variables that influence the achievement of the Sustainable Development Goals (SDGs), especially health governance. This study analyzes governance in Mexico’s health sector in relation to SDG 3 (Good Health and Well-being), using a qualitative and documentary methodology based on literature on institutional capacities, health system characteristics, and available indicators. Significant limitations were identified: information is incomplete, heterogeneous, and not timely, which hinders decision-making. There are disparities between subsystems in terms of budget and coverage, as well as a lack of continuity due to changes in government every six years, which impedes collaboration among system actors. The Mexican Social Security Institute bears the greatest burden in the system, despite limited human resources and infrastructure. The lack of coordination, weak governance, and social determinants of health highlight the urgency of a more comprehensive approach. Despite these weaknesses, progress has been made in reducing maternal and infant mortality. The study concludes that strengthening governance is key to achieving health objectives.