The Championship club confirmed the news on their official website on Tuesday night, with the 40-year-old replacing Jose Riga in the dugout at the Valley.
Riga left Charlton at the end of the season at the end of the short-term deal he was given to replace Chris Powell.
Peeters has previously managed Cercle Brugge and Gent and lands in England fresh from keeping Waasland-Beveren in the Belgian Juplier League.
He scored four goals in 13 appearances for his country, with his playing career taking in the likes of Roda JC, Vitesse Arnhem and Genk.
Peeters will be assisted by former academy manager Damien Matthew, with ex-assistant boss Alex Dyer leaving the club.
Dyer was a lieutenant of Powell, with the two guiding Charlton to the League One title in 2012 with a record-equalling 101 points.
- Sports & Recreation
- Jose Riga
- Cercle Brugge
- Chris Powell