Rafferty studied at Phillips Academy in Andover, Massachusetts, and graduated in 1989. She majored in English and Theatre at Hamilton College, studied theatre abroad in the United Kingdom and at the University of Oxford during her junior year, and, after graduating magna cum laude from Hamilton in 1993, went on to study at the Yale School of Drama, receiving a Master of Fine Arts.
She and her Suits co-star Gabriel Macht have been friends for over 20 years. They met in 1993 at the Williamstown Theatre Festival.
Rafferty met her husband Aleksanteri Olli-Pekka Seppälä, a stock research analyst in the asset management unit of Lazard Frères & Company in New York, and they were married on June 23, 2001, at the Roman Catholic church of St. Mary in Greenwich, Connecticut. The couple have two daughters, Oona Gray (b. 22 October 2007) and Iris Friday (b. January 2012).