This paper aims to discuss the issue of the judicial protection of human rights in post-conflict Burundi. In doing so, it provides some insights into Burundi’s legal and institutional framework. It further assesses this framework through the prism of the efficiency of institutional safeguards provided for by this framework, particularly the judiciary, as the cornerstone, both of human rights protection and of rule of law. While recognizing some merits of this framework, this reflection focuses on the main challenges faced by post-conflict Burundi’s judicial system in the protection of human rights. It argues that while it is far from perfect, Burundi’s legal framework is progressive and likely to ensure respect and protection of the human rights, provided there is positive and courageous enforcement by independent and competent judges. Given the current state of affairs, however, Burundi’s judiciary is institutionally too weak to properly perform its constitutional duty, especially with regards to its role of custodian of the citizen’s rights and freedoms. The paper suggests, accordingly, that this weakness is more a result of the lack of independence of the judiciary and the failure to adhere to the rule of law in practice, rather than a consequence of a legal vacuum of human rights protection.