Xenophobia remains a significant challenge within Africa, undermining the continent’s efforts to harness its vast human, economic, social, and political potential. Prejudices and biases based on perceived political, economic, or social disadvantages hinder mutual cohabitation between nationals and migrants, posing threats to national stability, territorial integrity, and socio-cultural cohesion. This study examines intra-African migration through the lens of natural law theory, emphasizing the moral and legal imperatives for protecting the inalienable rights of all individuals while fostering peaceful coexistence. The paper argues that sustainable development and harmonious social evolution require justice systems that safeguard citizens’ rights while actively countering discriminatory ideologies and practices, such as xenophobia. By analyzing the socio-political and economic consequences of exclusionary attitudes, the study highlights the need for policies and legal frameworks that promote inclusion, social justice, and equitable access to opportunities. It further explores how recognition of shared rights and responsibilities among African states can strengthen regional cooperation, stability, and progress. Ultimately, this research contributes to understanding the intersection of migration, human rights, and ethical governance in Africa, advocating for strategies that reconcile national interests with the protection of migrant communities. It underscores that eliminating xenophobic practices is not only a moral and legal necessity but also a prerequisite for the holistic advancement of African nations.