The agency will move into temporary offices while its new headquarters are being built. It is the second EU agency to leave Britain as a result of the UK's pending divorce from the bloc.
The Netherlands rolled out the orange carpet for European Medicines Agency Executive Director Guido Rasi on Wednesday, presenting him with a pair of clogs to mark his agency's relocation from London to Amsterdam.
The EMA'S new €300 million ($346 million) headquarters is currently under construction, so its 900 employees will first work out of temporary offices near the city's main train station until November.
The EMA, which is the EU's regulatory agency for the quality and safety of medicine, was forced to move as a result of Brexit. Amsterdam beat out Milan in a tiebreak vote to host the agency in November 2017.
The EMA is the second EU agency to make such a move. The European Banking Authority has relocated to Paris as a result of Brexit as well.
'Today is a good one'
Speaking at Wednesday's ceremony, EMA Director Rasi said: "So far [the move has gone] smoothly, so far everything is working. It's painful, it's hard, there's a lot of additional work … but it's going smoothly. I'm satisfied. Today is a good one!"
The Dutch have sought to win over businesses and agencies by touting their tax advantaged and business-friendly English-speaking environment. Moreover, they have tailored their pitch to the British, stressing, "we also have a very stylish queen, and enjoy fish and chips."
Speaking at a separate event alongside visiting Japanese Prime Minister Shinzo Abe, Dutch Prime Minister Mark Rutte welcomed such relocations, but stressed: "Brexit is not good and a hard Brexit could be even worse, and that could never be offset by extra investments from other countries."
The EMA has been based in London's Canary Wharf since 1995.
js/rc (AFP, AP, dpa)