Bilateral relations between Flanders and Lithuania have existed since the Middle Ages thanks to trade contacts between the two in the Hanseatic League. More recently, in 1996, a cooperation agreement was signed covering all areas over which Flanders has jurisdiction, and this was crystallised for three years in the form of a triennial work programme. 2016 marked the occasion of the twentieth anniversary of this agreement, which was celebrated with numerous cultural, academic and economic events, and Prime Minister Geert Bourgeois also visited Vilnius. He then opened a Flanders Investment & Trade office. Lithuania was also a major beneficiary of the Flemish Central and Eastern Europe Cooperation Programme, where Flemish and Lithuanians from all kinds of disciplines worked together as partners on projects. 

Since 1992, Central and Eastern Europe has been a priority partner region in the Flemish foreign policy of all successive Flanders governments. Close and in-depth links have been established through treaties, projects, exchanges, and cooperation programmes. Thanks to the established networks and contacts with the Baltic States, and to foster lasting approval and confidence, Minister Bourgeois decided to add Estonia, Latvia and Lithuania to the operational area of the Flemish Representation opened in Warsaw in October 2007.