The chapter discusses the challenges of horizontal and vertical coordination in Lithuania, one of the three Baltic countries that experienced the extensive economic and political transition from the Soviet system. Previous research on the Lithuanian self-governance system has focused on municipal performance and local autonomy, legislative reforms, decentralisation policy, and the efficiency of local governmental institutions in terms of public service delivery efficiency and scope. This chapter contributes to the academic discourse on the autonomy of local structures by discussing the interplay between vertical and horizontal coordination and how they affect Lithuania’s national multi-level self-governance structure. With a focus on a trend towards multi-level governance and enhanced bottom-up engagement, it is critical to consider the impact of regional policy and the willingness of local authorities to cooperate. Further research must thoroughly consider the relationship between regional demographic disparities and the necessity of efficient inter-municipal cooperation, responding to the central government’s shortcomings in linking territorial cohesion with equal access to public services and infrastructure.