Chikungunya virus poses a significant public health challenge in Indonesia. Robust surveillance and diagnostics are lacking, and clinical management guidelines (CMGs) are absent.This practice article draws on insights from a qualitative health system stakeholder study conducted in Jakarta and Bali, Indonesia. The study examined barriers to the development and implementation of chikungunya CMGs.Findings reveal critical gaps in knowledge, diagnostic tools and prioritisation, exacerbated by systemic decentralisation and resource limitations. Robust, locally adapted CMGs could address these gaps, enhance clinical care and improve outbreak preparedness. This study underscores the importance of stakeholder engagement and capacity building in developing CMGs, offering lessons for low-resource settings managing emerging diseases.