Background <p>Women’s healthcare decision-making autonomy in Somalia is essential for empowerment and viewed as a fundamental human right. In fragile states, local socio-cultural structures and gatekeeping norms uniquely influence the typical drivers of agency, such as education and wealth. This study provides the first national analysis of the levels and determinants of healthcare autonomy among married women using data from the 2020 Somalia Demographic and Health Survey (SDHS).</p> Methods <p>We analyzed a nationally representative sample of 7,492 married women. A multilevel mixed-effects binary logistic regression model was employed to account for the hierarchical structure of the data, with individuals nested within primary sampling units (PSUs). Autonomy was conceptualized using a relational framework and defined as meaningful participation in healthcare decisions (either alone or jointly).</p> Results <p>Overall, 67.1% of women reported healthcare autonomy. A “Permission Paradox” was identified: women reporting that obtaining permission was a major barrier had significantly higher odds of autonomy (AOR = 1.79; 95% CI: 1.43–2.23; <i>p</i> &lt; 0.001), suggesting that agency in this context is a negotiated process. Conversely, an “Education Anomaly” was observed, whereby secondary education was associated with a 41% reduction in the odds of autonomy (AOR = 0.59; <i>p</i> = 0.001). Regional context emerged as the strongest predictor; women in Bakool had nearly 4.5 times higher odds of autonomy (AOR = 4.47; <i>p</i> = 0.001) compared to those in Awdal.</p> Conclusion <p>Healthcare autonomy in Somalia represents a negotiated agency embedded in geospatial heterogeneity. One-third of women remain entirely excluded from health-related decisions. Policy responses should move beyond individualistic models toward decentralized, culturally grounded interventions that address structural gatekeeping and regional disparities to advance meaningful health equity.</p> Trial registration <p>Not applicable.</p>