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Background Indonesia is the third country in Southeast Asia with the highest maternal mortality ratio. In its remotest area, Papua, pregnant women still face limited access to safe delivery in health facilities, despite being covered by national health insurance. Objective This study examined the factors associated with institutional delivery in the Papua Region, Indonesia. Methods This cross-sectional study analysed 2,275 women aged 15 or older who had given birth in the last five years. The outcome variable was institutional delivery, while nine independent variables were assessed: province, residence, age, marital status, education, employment, wealth, parity, and completeness of antenatal care (ANC). Binary logistic regression was used to identify associated factors. Additionally, a Geographic Information System (GIS) was employed to map disparities in institutional delivery across the region. Results The overall coverage of institutional delivery in the Papua Region was 50.1%. Coastal areas showed higher prevalence, while the Central Mountains region had the lowest coverage. Institutional delivery was significantly associated with all nine independent variables. Women with lower education and without partners were less likely to deliver in health facilities, even when financially covered by health insurance. Conclusions The findings suggest that a combination of demographic, socioeconomic, and healthcare access factors influences the use of institutional delivery in Papua. Improving access requires multisectoral strategies, including infrastructure development, health education, and equitable healthcare delivery, particularly for women in remote and underserved areas.