Unless women get paid less because they are perceived to be less competent than men.
Let's look at some common justifications for paying women less, as taken, for instance, from the second Freakonomics book.
Women may go on maternity leave.
Women can't devote themselves 100% to the job because they have to care for children or the elderly.
Women are more nurturing, so they should be given support jobs, rather than jobs that bring in the revenue.
Women tend to go into lower-paid professions such as teaching, customer service, nursing, rather than engineering, finance, or surgery.
All of these are facts corroborated by statistics. Does that mean these statistics don't display discrimination? Some of these differences are biological - women can carry fetuses, men can't. Some of them are social. For instance, why is it that in most countries, maternity leave is only available to women? Why is it that we expect women to care for their families (i.e. do unpaid, often unrecognized work that nevertheless is extremely important and of huge benefit to society), and not men? Are women naturally more nurturing, or are they conditioned to be more nurturing? Employers respond to these assumptions about women by paying them less. Does that mean that they are doing wrong by acting in their self-interest? No, that's inconsistent with economic theory. However, it does mean that gender discrimination exists, it is based on extra-biological factors, and this situation can, in theory, be changed. tl;dr the gender pay gap is a fact, that's all.
Corollary: some papers like to "disprove" the pay gap by putting in control variables for stuff like number of raises, employee evaluations, awards, etc - but it is reasonable to assume that, if a company discriminates on pay, it will also discriminate on bonuses. There is a huge collinearity issue when you combine these variables with gender, because gender discrimination exists in all these spheres.