The Customs System of the Republic of Croatia has not lost its importance, the sole change that has taken place to its adjustment to international politics and different interests. Significant changes within the Customs System of the Republic of Croatia happened with the accession to the European Union. The role of customs has changed throughout history, going from a fiscal character to being shaped into a special instrument to protect national borders, including European borders, by leaving CEFTA. From the above facts arises the issues of this research, which deals with the organization and structure of the Customs system and also the Customs Administration through the period of time and therefore the period of accession to the European Union. All changes within laws and regulations are made at the extent of the European Union and in such circumstance Croatia strives to regulate customs policy, work and activities of customs so as to attain positive results. The aim of this paper is to analyze the changes that occurred during the accession to the European Union, to indicate the institutional structure and functioning of the Customs System, especially within the context of the union within the EU. Additionally, the aim is to look at the results of the Coronavirus pandemic on the functioning of the Customs System. It is emphasized that everyone’s tasks and activities undertaken by the Customs Administration of the Republic of Croatia must be guided by the instructions and guidelines of the European Union. Also, the recommendations sent to the regional and central customs offices for coping with the new circumstances are analyzed. In the end, it is often concluded that Croatia, through its membership within the Common Market, has gained relief in customs clearance of products and services, tax and relief reductions which it's established strong coordination by applying the recommendations and laws of the European Commission and control of imports and exports during a Coronavirus pandemic.