The 44-year-old takes charge of the Danish club’s youth team but will also have an input in the senior side – who meet the Whites in a pre-season friendly on Thursday night.
Frandsen was promoted to head coach of HB Køge in 2012, taking the club to sixth place in the First Division last term.
And the former midfielder, who made 304 appearances for Wanderers in two spells, is looking forward to the next chapter of his career.
“I’ve been happy with my five good years in HB Køge,” he said. “First as an assistant and then as head coach. I think we played a good and positive brand of football and am pleased to have helped to develop many young talents in HB Køge.
“It’s been a good time in my development as a coach and I will definitely miss the people in and around the club. Both players, coaches, managers, administration, the many volunteers and especially the fans.
“I look also forward to the new challenge, where I get the opportunity to help develop a lot of young players and make them ready for the first team of one of the country’s top clubs.”