The 26-year-old Brazilian-born player made only two starts for Arsenal this season and two brief appearances as a substitute following the serious leg injuries he sustained against Birmingham City in a Premier League match 15 months ago.
He suffered a broken fibula and dislocated ankle and there were fears he might not play again. The injuries kept him sidelined for almost a year.
"Eduardo underwent simple revision surgery on his left ankle earlier today," Arsenal said on their website. "The operation went well and Eduardo will follow a dedicated rehabilitation programme throughout June."
The statement added he is expected to return to full training in pre-season with the rest of the squad.
Earlier this week, Eduardo was left out of the Croatia squad to face Ukraine in a World Cup Group Six qualifier on June 6 because he is now recovering from a thigh strain.
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