Dr. Novacek's studies concern patterns of evolution and relationships among organisms, particularly mammals. His interests have ranged from paleontological evidence to new data on DNA sequences. He has led paleontological expeditions to Baja California, Mexico; the Andes Mountains of Chile; and the Yemen Arab Republic in search of fossil mammals and dinosaurs. He also is one of the team leaders of the joint American Museum of Natural History/Mongolian Academy of Sciences ongoing expeditions to the Gobi Desert, begun in 1990. The Mongolian expeditions marked the first return of a Western scientific team to the country in over sixty years and have received worldwide scientific and public attention for their spectacular findings. In 1993, Dr. Novacek was one of the discoverers of the Gobi's Ukhaa Tolgod, the richest Cretaceous fossil vertebrate site in the world. In 1999, he started a series of expeditions to Patagonia, Argentina, to research dinosaurs, mammals, and other fossils.

As Senior Vice President and Provost, Dr. Novacek provides leadership to the curatorial staff and advises the President on the direction of scientific research at the Museum. He also has oversight of the Museum’s Exhibition program. Dr. Novacek was instrumental in establishing the Museum's Center for Biodiversity and Conservation, Institute for Comparative Genomics, and new research program in astrophysics. In 2006, the State Board of Education authorized the Museum to establish the first PhD program of any museum in the nation.

Dr. Novacek is the author of more than 200 titles, including articles in the international scientific journals Science and Nature. He has also authored popular books on the Gobi expeditions, Dinosaurs of the Flaming Cliffs (1996) and on his experiences in the field, Time Traveler (2002) (each recognized as a New York TimesNotable Book of the Year). He is also a contributor to Natural History, Scientific American, The Smithsonian, and Time magazine, and his research has been widely covered by the print and electronic media. His research has been supported by many agencies, including the National Science Foundation, National Geographic Society, The Sloan Foundation, The Eppley Foundation, and the International Research and Exchange Board (IREX). He is a Fellow of the American Association for the Advancement of Sciences (AAAS) and the American Academy of Arts and Sciences. In recognition of his worldwide explorations, he received the Roy Chapman Andrews Society Distinguished Explorer’s Award for 2003 and the Lowell Thomas Award from the Explorer’s Club in 2005. He received Honorary Doctorates from Long Island University in 1996 and Beloit College in 2006.