In 1989, Gelnovatch served as a part-time assistant coach under Bruce Arena with the Virginia Cavaliers. In 1995, he became a full-time assistant at Virginia. On January 3, 1996, Gelnovatch replaced Arena as head coach. He is most notable for leading the Cavaliers to the 2009 NCAA Division I Men's Soccer Championship where the Cavaliers won a penalty shoot-out against Akron. His teams have reached the NCAA tournament every year he's coached, except 2021. He has led the Cavaliers to three NCAA college cup appearances, four Atlantic Coast Conference tournament titles, and two Atlantic Coast Conference regular season titles. In September 1999, Arena appointed Gelnovatch as the head coach of the United States U-18 men's national soccer team.[8] In 1999 and 2002, he also served as an assistant coach with the United States men's national soccer team.