Wednesday's decision was made jointly by the European Parliament and the Council of the EU after a tough battle between nine aspiring cities around Europe.
In the end, Lille won the final vote against Rome, Italy, by 36 votes to 18, according to the news site Politico Europe. Also on the losing side were Bucharest, The Hague, Liege, Malaga, Porto, Warsaw and Zagreb.
"They (Lille) are very well prepared for this authority. French customs have long and extensive experience with customs issues," said the European Parliament's chief negotiator Dirk Gotink at a press conference in Brussels.
The agency is expected to have approximately 250 employees.
