Scott, 23, joined the Royals' academy aged eight and helped Kelly Chambers' side maintain their top-flight status last term, following promotion in 2015.
"I am absolutely delighted to have signed a new deal with my childhood club," Scott told the club website.
Manager Chambers added: "Her work ethic and tenacity adds a great dimension to our defence."
Reading Women defender Harriet Scott has signed a new deal with the Women's Super League One club until 2018.