After retiring as a player, Berntsen coached Figgjo, Bryne and Viking. Between 1986 and 1986, Berntsen was also the assistant coach of the Norwegian national team.
Viking club director
Between 1999 and 2004, Berntsen was the Director of Viking. After Viking manager Kjell Inge Olsen resigned on 13 April 2004, he took over as caretaker manager until 12 July 2004, when the club signed Roy Hodgson as their new manager. Berntsen then resumed his role as club Director. In late 2004 he was surprisingly offered the job as head coach of the Norway women's national football team from 1 January 2005 on, which he accepted.
Berntsen's first tournament with the national women's team was the 2005 UEFA Women's Championship which took place in June 2005 in England. He courted controversy by including 16 year old Isabell Herlovsen, the daughter of one of his former teammates on the Norway national team, in the squad. However, she scored two vital goals to keep Norway in the tournament. After mixed fortunes in the group stage, Norway played a memorable semifinal against Sweden which they won by 3–2 after extra time with a goal from Solveig Gulbrandsen. In the final against Germany, Norway lost 3–1. Berntsen led the national women's team through qualification to the FIFA Women's World Cup 2007 tournament in China, where they won their group by beating Canada and Ghana and drawing against Australia. In the quarter final against the hosts China, in front of 50,000 spectators, Norway won 1–0, the only goal being scored by Herlovsen. In the semifinal, the team lost to Germany by 3–0, and they then lost the third-place playoff 4–1 against the US to finish in fourth place. By virtue of their performance at the World Cup, Norway qualified for the 2008 Olympics. After the UEFA Women's Euro 2009, Berntsen resigned as coach of the women's national team.
Later years
On 11 February 2010, Viking announced that Berntsen was again hired as the Director of the club, nearly five and a half years after he resigned from the same position. Two years later, Berntsen was nominated and elected vice president of the Football Association of Norway which meant that he had to quit his position at Viking. After Viking's relegation from the Eliteserien and manager Ian Burchnall's dismissal from the club in December 2017, Berntsen made a surprising return to Viking, leaving his role as vice president of the Norwegian FA to take on the manager role at the club. He led Viking to a first place in the 2018 1. divisjon and were promoted back to Eliteserien after one season's absence. On 20 June 2019, Viking announced that Berntsen's contract had been extended with two more years, till the end of the 2021 season. In the Norwegian local elections, 2019 he was elected to a seat in Sandnesmunicipal council, representing the Labour Party.
