Sabeti went on to study biology at the Massachusetts Institute of Technology (MIT) where she was a member of the varsity tennis team and class president, graduating in 1997 with a major in Biology and a "perfect 5.0 average." At MIT, she began her research career in David Bartel's laboratory and also worked in Eric Lander's laboratory, created the Freshman Leadership Program, and worked as a teaching assistant. She was then a Rhodes Scholar at University of Oxford and completed her Doctorate in Evolutionary Genetics in 2002, and graduated summa cum laude with a Doctor of Medicine at Harvard Medical School in 2006, being the third woman to receive this honor since the school had begun accepting female students. The Paul & Daisy Soros Fellowships for New Americans supported her graduate studies. Initially, Sabeti planned to enter medicine and become a doctor; however, she decided to pursue research instead after completing medical school and discovering she preferred research to medicine.