Donald received a B.A. summa cum laude in Russian Language and Literature from Yale University in 1980. After working at the Laboratory for Computer Graphics and Spatial Analysis in the Graduate School of Design at Harvard University, he then attended MIT EECS, where he received his S.M. in EECS (1984) and Ph.D. in Computer Science (1987) under the supervision of professor Tomás Lozano-Pérez in the MIT AI Lab (Artificial Intelligence Laboratory). He joined the Cornell University Department of Computer Science as an assistant professor in 1987.
At Cornell, Donald received tenure in 1993, and served as associate professor of computer science at Cornell University until 1998.  While on sabbatical at Stanford University (1994-1996), he worked at Paul Allen's research & development and technology incubator Interval Research Corporation (1995-1997), where he and Tom Ngo co-invented Embedded Constraint Graphics. After moving to Dartmouth, Donald was the Joan P. and Edward J. Foley Jr 1933 Professor of Computer Science, Dartmouth College until 2006 when he moved to Duke University. Currently Donald is the James B. Duke Professor of Computer Science, Chemistry, and Biochemistry, in the Trinity College of Arts and Sciences at Duke University and in the School of Medicine, Duke University Medical Center. Donald was appointed William and Sue Gross Professor from 2006 to 2012, and was named James B. Duke Professor in 2012.
He is a fellow of the Association for Computing Machinery (ACM) and a fellow of the IEEE. Previously, he was a Guggenheim Fellow (2001–2002) and received a National Science Foundation Presidential Young Investigator Award (1989–1994). In 2015, Donald was elected a fellow of the American Association for the Advancement of Science (AAAS), for contributions to computational molecular biology.