This study examines the interaction between university autonomy and labor human rights in Colombia, considering the fundamental principles of the country’s education system. University autonomy, enshrined in the Political Constitution, grants higher education institutions the authority to define their curricula, select staff, manage resources, and establish internal regulations. Concurrently, labor human rights, supported by the Constitution, national legislation, and international treaties, aim to ensure fair working conditions for employees. Through a comprehensive analysis of jurisprudence, doctrine, and current legal norms, the study identifies issues arising from the intersection of these principles. It is observed that the management of university autonomy can, in certain circumstances, create tensions with labor rights, potentially leading to unstable employment conditions, the implementation of disciplinary measures that could be considered arbitrary, and restrictions on union freedom. These issues are not solely attributable to university autonomy but to the manner in which institutions and their managers apply this autonomy. The study aims to evaluate how the administration of university autonomy impacts the protection and promotion of labor rights in Colombia and highlights the importance of reviewing statutory norms, promoting social dialogue, training university actors, and strengthening labor protection mechanisms.