Nepal's health sector vulnerabilities were exposed during the 2015 Gorkha earthquake, which prompted immediate reconstruction efforts. This disaster underscored the need for enhanced healthcare infrastructure throughout the country but encountered numerous challenges. This study aims to investigate the challenges faced during the post-earthquake reconstruction of health sector building projects in rural Nepal. Five major challenges were identified through a literature review, namely "resource challenges", "legal challenges", "physical and territorial challenges", "management and coordination challenges" and "social and cultural challenges". Perceptions on identified challenges were collected from 137 clients, consultants, and contractors working on 106 ongoing building construction projects in 9 districts across 3 provinces funded by the Government of India. Structural equation modeling (SEM) using the partial least squares (PLS) method was conducted with SmartPLS version 3 to identify the major challenges. All five challenges were found to be significant, with "resource challenges" being the most significant (β= 0.613), followed by "legal challenges", "physical and territorial challenges", "management and coordination challenges" and "social and cultural challenges". Based on these findings, it is suggested that Nepal should adopt a comprehensive strategy that includes proper resource management, improved legal frameworks, effective coordination between stakeholders, and an understanding of social and cultural dynamics to overcome these challenges. Therefore, all project stakeholders must collaborate to address these challenges, which will ensure a resilient and sustainable healthcare infrastructure in earthquake-prone regions like Nepal.