Mayer married lawyer and investor Zachary Bogue on December 12, 2009. On the day Yahoo! announced her hiring, Mayer revealed that she was pregnant; she gave birth to a baby boy on September 30, 2012. Although she asked for baby name suggestions via social media, she eventually chose the name Macallister from an existing list. On December 10, 2015, Mayer announced that she had given birth to identical twin girls, Marielle and Sylvana.
Mayer is Lutheran, but she has said—referencing Vince Lombardi's "Your God, your family and the Green Bay Packers"—that her priorities are "God, family and Yahoo!, except I'm not that religious, so it's really family and Yahoo!."