The final round of voting by EU ministers resulted in a tie between Amsterdam and Milan.
The capital of the Netherlands was selected after the drawing of lots, according to diplomatic sources.
It will become the host city to the EU medical regulator once Britain leaves the EU.
The EMA is one of several European agencies set to leave London and move elsewhere in Europe ahead of Brexit.
The European Banking Authority is also set to relocate, with cities including Dublin and Prague bidding to host the regulator.
This is a developing story. More to follow.