The truth is, the pay disparity grows over time. People are hired on based on the existing pay scale without regard to sex, but as women take time off to have children, or decline work that involves travel, or opt for flexible schedule over higher income, the disparity grows. To generalize, men are in it for the money and give up more for the job. Women want flexibility and benefits more than money.
In studies that take all variables into account — time continuously in the workforce, seniority, hours worked per week, etc. the gender pay gap either disappears or shrinks to a couple of percentage points.
This article describes what’s really happening: http://www.politifact.com/punditfact/statements/2014/apr/09/genevieve-wood/what-pay-gap-young-women-out-earn-men-cities-gop-p/
Colleges have become increasingly hostile places for men and the majority of students are now women. Increasingly, that is true of faculty, and women have an inside track to management in academia. The net result is that, increasingly, women are dominating the entry level jobs that require college so that, overall, young childless women outearn men in urban areas. That will slowly spread to the whole country and, due to seniority, as women get older, the average woman will outearn the average man.