The educational system of Lithuania has undergone transformation conditioned by the radical change of the political situation in the region after the restoration of independence on March 11, 1990. The new educational system was gradually developed, changing and denying the former Soviet educational framework. The main goal of the new educational system is to provide education compatible with the newly applicable international standards and create an effective network of schools. The article aims to present an overview of the reform of the institutional system of general education of Lithuania that began in 1988 and was to be completed in September 2015; however, the completion of the reform was recently postponed until September 2017. The article also reviews key challenges to the reform implementation and discusses the compatibility of the reform with societal expectations and standards of international educational law.