Milan, Amsterdam and Copenhagen first went after the first round of voting for where the EMA will be relocated following the UK's vote to leave the EU, according to reports from the meeting in Brussels.
Foreign affairs and EU ministers cast a secret ballot on Monday afternoon, but Sweden, one of 19 countries that had put itself forward, got knocked out in the first round of voting.
Copenhagen then lost the second round. Milan and Amsterdam received 13 votes each in the third round, with Amsterdam emerging as the winner after a coin toss.
Sweden had been courting the EMA following the Brexit vote in the United Kingdom, hoping to take the EU medical watchdog currently headquartered in London's Canary Wharf and employing around 900 people.
In May, Sweden launched a website detailing reasons why the agency should move there, boasting about Stockholm's public transport and flight connections, the country's high ability in English, and also lifestyle factors like Stockholm's nature and the Swedish work-life balance, on top of its booming tech scene.
However, southern Swedish region Skåne, which is closely connected to Denmark via the Öresund Bridge, put its support behind Copenhagen.