Former Liverpool defender, who ended his playing career in 2016, will begin his managerial career with HB Koge from the start of next season.
Beginning and ending his career with Danish club Brondby, Agger spent eight years at Liverpool, making 232 appearances and winning the League Cup in 2012. However, a series of unfortunate injuries forced him to cut his career short.
In addition to his career with the Reds, Agger won 75 caps for Denmark and captained them at the European Championship in 2012. He will be joined at Koge by former national team-mate Lars Jacobsen with contracts until the summer of 2024.
"HB Koge is the perfect place for me to start," Agger said.
"The club has healthy values and a solid foundation. I am very much looking forward to getting started - and yes, I look forward to coming under pressure again."
Agger will try to help Koge earn a promotion to the Danish top flight.