Andersen became youth manager of FC Luzern and returned to Germany again to manage the then-second tier team Rot-Weiß Oberhausen from 2003 until 2004.
After that spell he assisted Horst Köppel at Borussia Mönchengladbach.

In May 2007, he signed to Greek top-flight team Skoda Xanthi to manage them from 2007–08 on, but in June 2007 the contract was dissolved for private reasons.

In late 2007, he signed for 2.
Bundesliga strugglers Kickers Offenbach, but was unable to save them from relegation.

On 20 May 2008, he signed a two-year deal with 2.
Bundesliga outfit Mainz 05, and under his reign the team achieved promotion to the Bundesliga.
Despite the team's success, Andersen was fired on 3 August 2009.

Mid December 2010, he was named manager of the Greek Super League team Larissa.
After on 24 days in office, where the team lost three league matches and was knocked out of the cup competition, without scoring a single goal, he was let go.

Six months later, Andersen returned to Germany take charge of second division side Karlsruher SC.

Andersen became manager of Austria Salzburg on 2 January 2015.

After leaving Austria Salzburg in December 2015, Andersen was appointed as manager of North Korea in May 2016.
It marked the first time North Korea had appointed a foreign manager since 1991.
In 2018, he departed away from North Korea after two years working with the team.

In June 2018, he was announced as the new manager of South Korean side Incheon United, in the K-League.
He was sacked on 15 April 2019 with Incheon at the bottom of the table after collecting just four points from seven matches.
Andersen became youth manager of FC Luzern and returned to Germany again to manage the then-second tier team Rot-Weiß Oberhausen from 2003 until 2004. After that spell he assisted Horst Köppel at Borussia Mönchengladbach.
In May 2007, he signed to Greek top-flight team Skoda Xanthi to manage them from 2007–08 on, but in June 2007 the contract was dissolved for private reasons.
In late 2007, he signed for 2. Bundesliga strugglers Kickers Offenbach, but was unable to save them from relegation.
On 20 May 2008, he signed a two-year deal with 2. Bundesliga outfit Mainz 05, and under his reign the team achieved promotion to the Bundesliga. Despite the team's success, Andersen was fired on 3 August 2009.
Mid December 2010, he was named manager of the Greek Super League team Larissa. After on 24 days in office, where the team lost three league matches and was knocked out of the cup competition, without scoring a single goal, he was let go.
Six months later, Andersen returned to Germany take charge of second division side Karlsruher SC.
Andersen became manager of Austria Salzburg on 2 January 2015.
After leaving Austria Salzburg in December 2015, Andersen was appointed as manager of North Korea in May 2016. It marked the first time North Korea had appointed a foreign manager since 1991. In 2018, he departed away from North Korea after two years working with the team.
In June 2018, he was announced as the new manager of South Korean side Incheon United, in the K-League. He was sacked on 15 April 2019 with Incheon at the bottom of the table after collecting just four points from seven matches.
Jørn Andersen