The Agency is a centralized administrative structure with the Minister of Finance.

The Agency is a legal entity - second level spending unit of budget appropriations with the Minister of Finance, having its seat at 47, G.S.Rakovsky Str.  

The funding of the Agency is formed by budget appropriations and the revenues under Art. 14 of the Law on Customs, of which the Agency is an administrator.

The Agency is structured in Central Customs Directorate and regional customs directorates in Bourgas, Varna, Plovdiv, Rousse and Sofia.

 The regional customs directorates are managed by directors, who are directly responsible for the activity of the respective regional customs administrations.

The total staff number of the National Customs Agency is 3 768.

The staff of the Central Customs Directorate totals to 447.

Within the frames of the total staff number of the National Customs Agency, one representative is appointed to each of the following: the Permanent Representation of the Republic of Bulgaria to the European Union in Brussels, Belgium, to the World Customs Organisation in Brussels, Belgium, and to the Regional centre for combating trans-border crime with the South-east Cooperative Initiative, based in Bucharest, Romania.

The administration of the Central Customs Directorate is organized in 3 directorates of general administration, 7 directorates of specialized administration, Inspectorate, Information Security Unit and Internal Audit Unit.

The organization and activity of the regional customs directorates are set by regulations, adopted by the Minister of Finance, proposed by the Director of the Agency.