Mackovic's coaching career began at Miami University in Ohio as a graduate assistant in 1965. He then served stints as offensive coordinator at San Jose State University and the University of Arizona before serving as offensive coordinator and assistant head coach at Purdue University in 1977. In 2006, Mackovic again returned to coaching when he was named as the head coach of the U.S. national team. He led Team USA to win the 2007 IFAF World Cup in their first appearance in the American Football World Cup held in Kawasaki, Japan.