The Argentine -- City's record goalscorer -- has been troubled by a problem in his left knee for the past five weeks.
On Friday, City boss Pep Guardiola admitted he was unsure when the 29-year-old, who has scored 30 goals this season and 199 in total for the club, would be fit again.
Aguero has now had keyhole surgery in a bid to resolve the issue.
"Recovering from an arthroscopy on my knee," he tweeted. "Fully motivated to get back soon to the field."
No timescale for his recovery has been given but, with City already crowned Premier League champions, the World Cup in Russia, which starts in June, will be his main target.
Aguero has not started a game since City's victory over Chelsea on March 4, although he was an unused substitute against Basel on March 7.
Following a month-long lay-off he returned to action as a late substitute in the derby defeat to Manchester United on April 7, when he was hurt in a controversial challenge from Ashley Young that went unpunished.
After that he was unable to train fully in the build-up to the second leg of City's Champions League quarter-final against Liverpool on April 10. Again, he was only able to appear as a second-half substitute.
With the issue still bothering him, he was ruled out of last Saturday's 3-1 win at Tottenham, with Guardiola casting doubt over whether the forward would play again this season.
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