Jernej Ule was born and raised in Ljubljana, Slovenia. He obtained his Ph.D. from the Rockefeller University in New York in 2004 with Robert B. Darnell, where he remained as a postdoctoral fellow until June 2006. He then started his own research group at the MRC Laboratory of Molecular Biology in Cambridge, UK, where he stayed until 2013.
In April 2013, he moved with his research group to the UCL Institute of Neurology, where he is a professor at the Department of Molecular Neuroscience. His group was seconded to the Francis Crick Institute in 2016.