Intergovernmental relation is a necessary political tool for mutual intertwines among the levels of government for the realization and facilitation of government goals and objectives. Intergovernmental wrangling has been a morphological characteristic of Nigerian federalism. The 1999 Nigerian constitution stipulates unequivocal and unambiguous demarcation of functions, powers and jurisdictional ecology within the purview of Nigerian political framework. However, lack of economic justice occasioned by jurisdictional scruples tortured intergovernmental relations during the political regime of former President Olusegun Obasanjo administration in the fourth republic in Nigeria. This study therefore x-rayed chronological crusades of intergovernmental relation conflicts and resource control in the fourth republic in Nigeria. Methodology employed in this study was derived from secondary sources of data collection, such as: newspaper reports, textbooks, and academic journals. It also adopted interactive and conflict resolution theory to re-echo how best to manage intergovernmental relation conflicts in Nigerian federal-state. This work concludes that intergovernmental relation is a necessary political synergy for the actualization and implementation of government policies and programmes. Therefore, justice, fairness and equity in the allocation of economic resources that endure tolerance and cooperation are veritable weapons to mitigate intergovernmental relation conflicts in Nigerian federalism.