Six cases of cerebral venous sinus thrombosis (CVST) occurred in the United States, in most cases in combination with low levels of blood platelets.
A week ago, Johnson and Johnson had started shipping the vaccines to countries in the European Union.
The company then called for the rollout to be delayed to give time for clarification.
However, the EMA said that the vaccine could be used without restriction and that the benefits of the jab in preventing Covid-19 outweighed the risks of side effects.
US regulatory authorities suspended use of the vaccine a week ago, after some 6.8 million people there had received the jab.