Returning to Denmark, Nielsen worked as a high school teacher for several years. From 1975, Nielsen lectured at the Institute for English at Odense University. He received his PhD in November 1980 with the thesis Old English and the Continental Germanic languages, which has subsequently been published in several editions. In 1999, Nielsen was appointed Professor of Historical Linguistics at the University of Southern Denmark. He retired as Professor Emeritus in September 2006, but continued to teach and research until his death in 2021.