The Brazil international picked up the ailment in The Gunners 3-1 defeat to Olympiakos in Greece last week, with initial reports indicating that the defender would be out for only three weeks.
However after further examination, it turns out the former Fenerbahce man has damaged ligaments and must go under the knife.
“Arsenal Football Club can confirm that, following investigations and subsequent medical opinions by club specialists, left-back Andre Santos will have surgery to repair ligament damage in his right ankle sustained in the game against Olympiakos last week,” a statement on the club’s official website reads.
“Andre will have surgery in Brazil this week and is expected to be out for around three months. Everyone at the club wishes him well.”
The news will be a blow for Arsene Wenger, who has seen all his first team full backs pick up injuries of late.
Bacary Sagna is still in rehabilitation after breaking his leg, Kieran Gibbs has had a hernia operation and Carl Jenkinson is sidelined with a stress fracture in his back.
The Emirates outfit fielded Johan Djourou and Thomas Vermaelen as full backs in the 1-0 win over Everton at the weekend, and will have to make do with centre halves playing out of position for the time being.
By Gareth McKnight