The 24-year-old pulled out of Arsenal’s starting XI against Stoke City shortly before kick-off with reports initially suggesting he was suffering from illness before it became clear he had pain in his stomach.
“Theo will be out for a few weeks,” said Arsene Wenger to the club’s official website.
“He has developed some damage to his posterior abdominal wall. It's not a hernia, but it's a little structural problem in his abdomen.
“He will have the procedure in Germany on Wednesday and, because it’s so minor, we can begin his rehab immediately. We are pleased it’s being dealt with quickly and he shouldn’t miss too many Arsenal matches. But he will miss the forthcoming international matches with England.”
England need to win their final two qualifiers to be guaranteed a spot at the 2014 World Cup in Brazil.
Walcott is also set to miss Arsenal’s Premier League matches with Swansea and West Brom as well as their Champions League tie with Napoli.