In the fall of 1980, Daugherty returned to America to pursue doctoral studies in composition at the Yale School of Music. During that time, Jacob Druckman (who was one of America's most influential composers) was chair of the composition department at Yale and composer in residence with the New York Philharmonic. Daugherty studied with Druckman and other Pulitzer Prize winning composers at Yale, including Bernard Rands and Roger Reynolds. He also studied improvisational notation systems and open form with experimental music composer Earle Brown. Daugherty's composition class at Yale included student composers who would later become unique and important voices in contemporary music: Bang on a Can composers Michael Gordon, David Lang, and Julia Wolfe; along with Robert Beaser, Aaron Jay Kernis, Scott Lindroth, and Betty Olivero.