Since joining the Cornell faculty in 1990 T.M. Duncan has received the Tien Prize for Teaching Excellence from the College of Engineering in 1994, the Paramount Professor Award from the Cornell Panhellenic and Interfraternity Council in 1995, and an Excellence in Teaching Award (Mr. and Mrs. Richard F. Tucker '50 Prize) from the College of Engineering in 2000. He was awarded the Tau Beta Pi / Cornell Society of Engineers Award for Teaching Excellence in 1997, 2008, and in 2013.

The American Indian Science and Engineering Society recognized Professor Duncan for 'outstanding teaching' in May 1997.

Professor Duncan was again honored by the Fraternity and Sorority Community in fall 2001. He again received the Outstanding Faculty Award for the College of Engineering.

In 2005 he earned the distinction of Weiss Presidential Fellow of Cornell University.

He was named a Merrill Presidential Scholar Mentor by Catherine Labelle in 1994, Rakesh Kadakia in 1995, Todd Zion in 1997, John Murphy in 1999, Leonid Shumuylovich in 2003, Eric Margelefsky in 2004, Michael Myers in 2009, Praveen Bagavandoss in 2019, Ellen Park in 2020, and Sarah Huang in 2022.

Professor Duncan received the James M. and Marsha D. McCormick Award for Excellence in Advising First Year Students in 2006, 2010, and 2018.

The Carnegie Foundation for the Advancement of Teaching and the Council for Advancement and Support of Education selected Duncan for the distinction of New York's Professor of the Year in 2007.

Duncan was recognized by Cornell University with a Kendall S. Carpenter Memorial Advising Award. in 2022, which recognizes sustained and distinguished contributions of professorial faculty and senior lecturers to undergraduate advising.