Stephanie Wilson was born in Boston, Massachusetts on September 27, 1966. About a year later, her parents, Eugene and Barbara Wilson, decided to move to Pittsfield, Massachusetts. Eugene, a native of Nesmith, South Carolina, used his electronics training from his time in the Navy to get himself a degree from Northeastern University and a long career in electrical engineering for Raytheon, Sprague Electric, and Lockheed Martin, while Barbara worked as a production assistant for Lockheed Martin. After attending Stearns Elementary School, she attended Crosby Junior High School. For a career awareness class in middle school, Wilson was assigned to interview someone in a field that interested her. Since she liked to look up at the sky, she interviewed Williams College astronomer Jay Pasachoff, , clarifying her potential career interest in space. In high school, Eugene encouraged Stephanie to go into engineering, so she decided to become an aerospace engineer. Wilson graduated from Taconic High School, Pittsfield, Massachusetts, in 1984. She attended Harvard University, receiving a bachelor of science degree in engineering science in 1988. Wilson earned a Master of Science degree in aerospace engineering from the University of Texas, in 1992. Wilson has returned to Harvard as a member of the Harvard Board of Overseers. She was the Chief Marshal for the 362nd Harvard Commencement on May 30, 2013.