The short answer is YES -- while some of the wage gap can be explained by choices, not all of it can.
According to the American Association of University WomenAmerican Association of University Women:
After accounting for college major, occupation, industry, sector, hours worked, workplace flexibility, experience, educational attainment, enrollment status, GPA, institution selectivity, age, race/ethnicity, region, marital status, and number of children, a 5 percent difference in the earnings of male and female college graduates one year after graduation was still unexplained.
A similar analysis of full-time workers 10 years after college graduation found a 12 percent unexplained difference in earnings. [emphasis in original]
Much more information, including information about the pay gap in many different countries can be found by following the links on this page from Radford University.
A chart from the U.S. Senate breaks down the pay gap into explained (by factors such as hours worked and experience) and unexplained. This is the Government Accounting Office report that explains where that chart comes from.
You can also see similar analysis in What Do Wage Differentials Tell Us about Labor Market Discrimination? from the National Bureau of Economic Research. A similar analysis from a nonprofit working to expand opportunities for women in business found similar results in 2010.