The 40-year-old arrives at The Valley from Belgian Pro League outfit Waasland-Beveren, having guided them to safety with a 14th-placed finish at the end of the 2013-14 campaign.
Peeters, who played 13 times for Belgium and scored four times, including a hat-trick against San Marino, takes over from Jose Riga.
Riga was appointed as a replacement for Chris Powell in March this year, and managed to secure the club's Championship status, but left at the end of the season when his short-term deal expired.
Before moving to Waasland-Beveren, Peeters had spells in charge of Cercle Brugge and Gent.
Peeters will work alongside current first-team coach Damien Matthew, but former assistant manager Alex Dyer has left the club.
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