Thostenson received a National Science Foundation Early Career Development Award (CAREER) in addition to a Young Investigator Program (YIP) Award from the Air Force Office of Scientific Research. He has led interdisciplinary research programs funded by the National Science Foundation and the Federal Highway Administration. Through the course of his research he received funding from ARO, AFOSR, ONR, NIH, NSF, and insustry. He received the Outstanding McNair Faculty Mentor Award and also received the Distinguished Young Alumni Award from his alma mater Winona State University. He is the recipient of the Elsevier Young Composites Researcher Award from the American Society for Composites recognizing researchers who early in their career have made a significant impact on the science and technology of composite materials through a sustained research effort. He was the recipient of the inaugural Hayashi International Memorial Award from the Japan Society for Composite Materials, recognizing outstanding young international researchers in the field of composites. During his graduate studies Thostenson received the Allan P. Colburn Prize for outstanding dissertation in the engineering and mathematical sciences (University of Delaware, Office of Graduate Studies).