Flannery has held various academic positions throughout his career. He spent many years in Adelaide, including a spell as professor at the University of Adelaide, and 7 years as director of the South Australian Museum. He was also principal research scientist at the Australian Museum, during which time he worked to save the bandicoot population on North Head. In 1999 he held the year-long visiting chair of Australian studies at Harvard University. In 2002, Flannery was appointed as chair of South Australia's Sustainability Board (South Australia).