Establishing an efficient transportation infrastructure is part of urban development and could benefit multiple aspects of modern life. However, with the rise in the population, traffic congestion has become apparent and transportation systems urgently need to be improved. This study investigates several challenges that hindered the implementation of the bus rapid transit system implementation in the perspective of a developing country. Expert opinions were gathered using the Delphi method to identify the challenges, while decision-making trial and evaluation laboratory (DEMATEL) and analytic hierarchy process (AHP) methods were used to analyze the interconnectedness of these challenges and prioritize them in terms of the urgency to mitigate them. A total of 18 challenges were listed covering internal and external factors. The results show that approval during planning, communication barriers between consultants and contractors, and political will of the government officials significantly influence other challenges. Moreover, approval during planning, complexity of implementation, complaints of the affected establishments, coordination between different agencies, and impact on public utility jeepney (PUJ) drivers are the challenges ranked highest in terms of prioritization. These findings will aid the stakeholders in managing the challenges and provide insights and guidelines for developing strategies to overcome them.