Athey studied economics, mathematics, and computer science at Duke University, Durham, N.C. (B.A., 1991), and economics at the Stanford University Graduate School of Business (Ph.D., 1995). She joined the economics faculty at the Massachusetts Institute of Technology, where she later held (1997–2001) the Castle Krob Career Development Chair. She returned to the Stanford Graduate School of Business as an associate professor of economics (2001–04) and then held the Holbrook Working Chair (2004–06). In 2006 Athey and her husband, econometrician Guido Imbens, accepted a joint offer from Harvard University, where Athey worked as a professor of economics.

Although Athey's work was extremely theoretical and complex, among other things it enabled economists to test their own predictions about how firms would behave in uncertain circumstances. Her “comparative statics” research into how economic variables alter when something in the environment changes identified the crucial economic assumptions on risk preferences and the nature of risk that allow a researcher to draw conclusions. Athey was affiliated with a firm that advised governments on auction design, and much of her research was concentrated in this area, in which individuals, firms, or governments actively specify and enforce the rules. From 1997 she was also associated with the National Bureau of Economic Research.

Athey was a member of the Committee for the Status of Women in the Economics Profession, and her desire to raise the status of women in her field was evident in her selection of 16 female economists for the committee to organize the 2006 winter Econometric Society meetings. Her extensive editorial interests were reflected in her involvement in many journals, including coeditorship of American Economic Journals: Microeconomics and associate editorships of Econometrica, Theoretical Economics, and the Quarterly Journal of Economics.