The 24-year-old is set to be sidelined for six months after suffering anterior cruciate ligament damage when making a defensive tackle in the FA Cup third-round win over Tottenham, which shattered his World Cup dream.
Wenger revealed the operation had gone "very well", and now it would be a case of everyone focussing on the player's long-term recovery.
"The damage was real in the knee so he will have to take the needed time, so let's not be hopeful that he will go to the World Cup - that is not possible, but overall his long-term future is very positive," Wenger said to Arsenal Player.
"It is about being fit for next season now."
As well as having to do without Walcott, the Barclays Premier League leaders have plenty of injury concerns ahead of Saturday's visit of relegation battlers Fulham.
Czech midfielder Tomas Rosicky could play in a protective mask after surgery to correct a broken nose suffered in the 2-1 win at Aston Villa on Monday night when he was caught by a stray elbow from Gabriel Agbonlahor, but full-back Nacho Monreal is a major doubt after twisting a ligament in his foot.
Captain Thomas Vermaelen (knee) is also sidelined, along with midfield duo Mikel Arteta (calf) and Aaron Ramsey (thigh). Striker Nicklas Bendtner could return from his ankle injury in the FA Cup tie against Coventry next Friday night.
Despite plenty of fitness concerns, Wenger still feels his squad has enough strength in depth, particularly in midfield, as the Gunners look to hold off Manchester City and Chelsea in the title race.
Alex Oxlade-Chamberlain, Kieran Gibbs and Lukas Podolski have all recently returned to fitness, boosting Wenger's options.
"In midfield we have plenty of quality players who you can rotate easily without really feeling, 'today we are weaker'," Wenger said.
"We have fantastic players in midfield and it always allows us to keep what we call the 'engine' of the team fresh.
"It is a real team effort. Maybe because every player in his position has a strong personality as well - you have that feeling.
"I would say purely on the football front it's true that we only have excellent players in every position and that allows you to have different types of teams that can really be efficient."
Following injury to Walcott, Arsenal are expected to move for some offensive cover during the transfer window.
Auxerre forward Paul-Georges Ntep has been touted as a potential target, along with Schalke's German forward Julian Draxler, who is said to have a £37million buy-out clause.
Wenger, though, concedes pushing through a permanent big-money deal is notoriously difficult at this stage of the season.
Gunners defender Per Mertesacker, though, would welcome another of his countrymen to the Emirates Stadium.
Speaking to German sports website, www.spox.com, Mertesacker said: "We already have a little German academy here and I learned that German discipline and talents are very appreciated here (at Arsenal).
"We would love to welcome a player like Draxler, he is so young and already plays a huge role in Schalke and in the national team."
Mertesacker added: "There is lots of talking about possible transfers, so I am curious about what is going to happen."