Penelitian ini dilatarbelakangi oleh meningkatnya beban administrasi pengelolaan Perjanjian Kerja Sama antara BPJS Kesehatan dan fasilitas kesehatan dalam Program JKN. Sistem kontrak manual masih menghadapi masalah keterlambatan penyelesaian dokumen, kebutuhan sumber daya besar, risiko kesalahan administrasi, dan kerentanan penyimpanan arsip fisik. Penelitian ini bertujuan menjawab apakah kontrak elektronik dapat meningkatkan efektivitas, efisiensi, dan keamanan pengelolaan kerja sama fasilitas kesehatan, serta apakah kepemilikan dan kelas rumah sakit memengaruhi implementasinya. Hipotesis penelitian menyatakan bahwa kontrak elektronik lebih efektif, efisien, dan aman dibandingkan kontrak manual, serta implementasinya dipengaruhi oleh kepemilikan dan kelas rumah sakit. Penelitian menggunakan desain non-eksperimental komparatif dengan pendekatan mixed-method. Unit analisis adalah pengelolaan dokumen kerja sama antara BPJS Kesehatan dan FKRTL. Data diperoleh dari data sekunder monitoring 2.650 rumah sakit, wawancara mendalam, dan observasi lapangan. Analisis dilakukan secara deskriptif dan inferensial menggunakan Mann–Whitney U dan Chi-Square, serta diperkuat dengan analisis kualitatif. Hasil penelitian menunjukkan bahwa hipotesis efektivitas terbukti karena kontrak elektronik lebih tepat waktu dan konsisten. Hipotesis efisiensi juga terbukti pada sebagian besar indikator, terutama biaya, durasi, beban kerja, dan rasio efisiensi waktu-biaya, meskipun indikator Time Efficiency Ratio tidak menunjukkan perbedaan signifikan. Hipotesis keamanan terbukti secara kualitatif melalui penyimpanan digital, tanda tangan elektronik, e-meterai, dan kontrol akses. Kepemilikan serta kelas rumah sakit juga terbukti berhubungan dengan implementasi kontrak elektronik. Kesimpulannya, kontrak elektronik lebih unggul dibandingkan kontrak manual dalam mendukung tata kelola kerja sama fasilitas kesehatan. BPJS Kesehatan disarankan memastikan  implementasi nasional, memperkuat pelatihan pengguna, keamanan akses, integrasi sistem, dan kebijakan teknis pendukung.

This study was motivated by the increasing administrative burden in managing Cooperation Agreements between BPJS Kesehatan and healthcare facilities under the National Health Insurance Programme. The manual contract system continues to face several problems, including delays in document completion, high resource requirements, administrative errors, and vulnerabilities in physical document storage. This study aimed to examine whether electronic contracts can improve the effectiveness, efficiency, and security of healthcare facility partnership management, and whether hospital ownership and class influence their implementation. The research hypotheses stated that electronic contracts are more effective, efficient, and secure than manual contracts, and that their implementation is influenced by hospital ownership and class. This study used a comparative non-experimental design with a mixed-methods approach. The unit of analysis was the management of cooperation agreement documents between BPJS Kesehatan and referral healthcare facilities. Data were obtained from secondary monitoring data involving 2,650 hospitals, in-depth interviews, and field observations. The analysis was conducted descriptively and inferentially using the Mann–Whitney U test and Chi-square test, supported by thematic analysis. The findings showed that the effectiveness hypothesis was supported, as electronic contracts were more timely and consistent. The efficiency hypothesis was also supported for most indicators, particularly cost, completion duration, workload, and the cost-time efficiency ratio, although the Time Efficiency Ratio indicator did not show a statistically significant difference. The security hypothesis was supported qualitatively through digital storage, electronic signatures, e-stamps, and access control. Hospital ownership and class were also found to be associated with electronic contract implementation. In conclusion, electronic contracts are superior to manual contracts in supporting the governance of healthcare facility partnerships. BPJS Kesehatan is advised to expand national implementation, strengthen user training, improve access security, enhance system integration, and develop supporting technical policies.