From 1978 to 1983 Quiggin was a Research Economist and in 1986 was the Chief Research Economist with the Bureau of Agricultural Economics what was of the predecessor of the Australian Bureau of Agricultural and Resource Economics of the Australian Government Department of Agriculture, Fisheries and Forestry.
He has been based at the University of Queensland since 2003, being an Australian Research Council Professorial Fellow and Federation Fellow and a Professor in the School of Economics and the School of Political Science and International Studies.