MacKinnon was born in Minneapolis, Minnesota, the first of three children (a girl and two boys) to Elizabeth Valentine Davis and George E. MacKinnon; her father was a lawyer, congressman (1947–1949), and judge on the U.S. Court of Appeals for the D.C. Circuit (1969–1995).[4]
She is the third generation of her family to attend her mother's alma mater, Smith College.[5] She earned her MSL and then a J.D. from Yale Law School in 1977 and a PhD in political science, also from Yale University, in 1987. While at Yale, she received a National Science Foundation fellowship.[6][1]