In 1971, Eggen became manager of Rosenborg, winning the league in his inaugural season. He left to take over Norway U21 in 1973. He then became national team manager for Norway jointly with Kjell Schou-Andreassen until 1977. He then returned to Rosenborg where he remained until 1982. He then coached Orkdal until 1985. In 1986, he was hired as manager for Moss, where he won the Second Division in the first season and then the top league the following. During this period he was also manager of Norway U23. He started managing Rosenborg in 1988, where he remained until 2002, except for a sabbatical in 1998. This is the team's golden age, resulting in 11 consecutive league titles and the participation in eight consecutive seasons in Champions League. Eggen returned a manager for the single 2010 season, again winning the league.