Using rich data on graduate tenure-track faculty, we explore the gender pay gap in academic departments of economics and agricultural/applied economics and the differences between them. We find that the gender pay gaps in economics and agricultural/applied economics are 8.3% and 4.1%, respectively, controlling for faculty rank, experience, and university affiliation. The gender pay gap increases with rank and varies across institutions. Productivity is an important determinant of wages but it explains little of the gender pay gap.While the lower unexplained gap in agricultural/applied economics is laudable, a greater share of women who are assistant and associate professors is part of the explanation. Given institutional differences, we explore the extent to which institutional factors-differences in the returns to observed characteristics, such as rank; unobserved characteristics; and institutional differences in pay levels-contribute to the gender pay gap.