Author of more than 80 scientific publications, Flynn's research focuses on the evolution of mammals and Mesozoic vertebrates, geological dating, plate tectonics, and biogeography. He also has contributed articles to Scientific American, Natural History, and National Geographic, provided scientific expertise for several popular science books, and been featured in numerous television and radio shows, newspapers and magazines. Dr. Flynn has led more than 3 dozen paleontological expeditions to Chile, Peru, Colombia, Madagascar, and the Rocky Mountains, supported by the U.S. National Science Foundation, the National Geographic Society, NASA, and other organizations. Flynn recently received a Guggenheim Fellowship for a year of research and expeditions in South American and has served as elected President (1999-2001) and member of the Board/Executive Committee (1993-2002) of the Society of Vertebrate Paleontology, the world's largest organization of professionals in this field.

With a specialty in mammalian paleontology and paleomagnetism, Flynn has spent his career searching for important new fossil mammal localities, as well as developing newer and more sophisticated ways to read the age of rocks and fossils, leading to more accurate geological time scales. He is actively pursuing laboratory research on the anatomy, DNA and evolution of Carnivora, and has current field programs focusing on the Andes Mountains of Chile, Amazon Basin of Peru, and Mesozoic deposits of Madagascar and India. In addition, Dr. Flynn has been deeply involved in integrating research with Museum exhibition and educational programs, and he recently embarked on helping to expand and enhance the world-leading fossil mammal collections at the American Museum.

On recent expeditions to the Andes Mountains in Chile, Dr. Flynn and colleagues discovered a number of extremely important and rare fossil specimens: the continent's oldest, best preserved fossil primate skull and oldest rodent fossils, both of which suggest an African origin for these important New World groups. These same Andean volcanic-derived deposits have produced at least 12 new mammal faunas, spanning at least 30 million years (~40-10 million years ago) and more than 4 degrees of latitude, including a newly named South American Land Mammal "Age" (the Tinguirirican) and evidence for the oldest open habitat/grassland environments found anywhere in the world. Similarly, 6 recent expeditions to Madagascar uncovered spectacular Mesozoic fossils, from mid-late Triassic cynodonts, archosaurs, and rhynchosaurs to tiny advanced mid-Jurassic mammals representing the oldest known tribosphenic mammals. Together with several doctoral students and postdoctoral scientists, Flynn's research also has focused on integrating molecular, anatomical and paleontological data in analysis of the phylogeny and diversification of major groups of mammals, and the investigation of the evolutionary relationships and patterns and rates of evolution of the mammalian order Carnivora (e.g. cats, dogs, bears, weasels, seals, etc.) and its extinct relatives.