Educational cooperation in higher education offers valuable opportunities for students and institutions alike. However, it also introduces significant challenges, particularly regarding student enrollment processes. Traditional centralized systems for managing this task can pose issues around authority, transparency, accountability, security, and cost, often hindering scalability and sustainable growth. This paper introduces the Cross-Institutional Blockchain Enrollment System (BCHEEN), a novel decentralized platform designed to streamline and enhance cross-institutional enrollment processes. Un-like existing solutions, BCHEEN employs a unique hybrid architecture that leverages blockchain technology to ensure transparency and security while maintaining scalability through innovative off-chain data management using the “replicate when used” approach. The platform was prototyped as a permissioned blockchain platform using the Hyperledger Composer framework and evaluated through functional, performance, and security analyses using tools such as Cucumber and Hyperledger Caliper. Evaluation results show that BCHEEN achieved a peak throughput of 18 tps at a send rate of 47 tps, with an average latency of 4.32 s under the same conditions, demonstrating its scalability and reliability. Furthermore, a computational cost analysis highlights the efficiency of the “replicate when used” approach in reducing storage overhead while preserving data integrity. BCHEEN’s practical impact includes streamlining enrollment processes, reducing administrative costs, and fostering secure, scalable, and transparent inter-institutional collaboration. These contributions position BCHEEN as a transformative tool for higher education, supporting policy advancements and promoting resilience and sustainability in educational practices.