The gender pay gap is 16.2 percent, the commission said. That is the average difference in hourly earnings between men and women.
That difference equals 59 days of work per year for free. Given a typical work week is five days long, that equals nearly three months of work.
The report was timed in advance of 2013 European Equal Pay Day, which is Thursday.
"The EU-wide event marks the extra number of days that women would need to work to match the amount earned by men: currently 59 days, meaning this year the day falls on 28 February," the commission said in a statement.
The event celebrates efforts around Europe to narrow the gender gap. This year, the commission noted German media firm Axel Springer AG launched an "Opportunities Equal" program that has a goal of increasing the numbers of women in managerial positions to 30 percent within 5-8 years.
Omnitel, a mobile communications company in Lithuania, has increased the numbers of its female managers by offering flexible arrangements meant to create "a family friendly work environment," the commission said.
The pay gap has declined slightly in recent years due to the economic downturn that has depressed earnings for men in various fields, such as construction, faster than it has for the labor market on the whole, the commission said.