"At the European level, we estimate that 5,000 to 6,000 individuals have left for Syria," the Justice Commissioner told Le Figaro in an interview, adding that the true number was likely to be far higher due to the difficulty of tracking foreign fighters in the conflict.
"At the time of the attacks in Paris and Copenhagen, we decided not to allow ourselves to be guided by fear," she said, referring to January's twin Islamist attacks in the French capital and the subsequent deadly shootings on a cultural centre in Denmark.
Focusing on those seeking to leave for Syria to wage jihad, or those returning from the conflict, meant intervening "too late", she said.
Jourová said the EU instead wanted to promote prevention as a means of curtailing the steady flow of European nationals, looking at the diverse reasons why people joined jihadist groups beyond simply religion.
British research had identified "a desire for adventure, boredom, dissatisfaction with their situation in life or a lack of prospects," in those who had opted to leave their families behind and head for Syria, the commissioner said.
Another focus for the EU was speeding up the exchange of information between the police forces and court systems of member states, she said, with more intelligence sharing required.
The self-proclaimed Islamic State (Isis), which rules a swathe of territory in Syria and Iraq it has deemed an Islamic "caliphate", has attracted thousands of foreign fighters, many from the West.
German Interior Minister Thomas de Maizière said last month that about 650 Germans have joined Isis fighters in Iraq and Syria.
Some 106 returnees suspected of having fought alongside IS jihadists are being investigated in Germany in 68 preliminary or criminal inquiries, chief federal prosecutor Harald Range told reporters last month.
Germany also has one of the highest numbers of fighters travelling to Syria and Iraq to join extremist groups, according to the most recent data from January by the International Centre for the Study of Radicalisation and Political Violence (ICSR), along with the United Kingdom and France.