Bukele said on social media that the goal was to "extract every last one" of the suspected gang members believed to be hiding in the 10 de Octubre area of San Salvador.
Defense Minister Rene Francis Merino said there were "indications that these criminals want to establish themselves" in the neighborhood.
Images released by the government showed soldiers massing for the operation and heavily armed police patrolling the neighborhood and checking identity documents.
According to Justice and Security Minister Gustavo Villatoro, the operation aimed to "continue destroying the criminal economy."
El Salvador has been under a state of emergency since March 2022 as part of Bukele's controversial "war" against gangsters.
Around 83,000 suspected gang members have been detained under the measures, which allow arrests without a court order.
The crackdown has led to a sharp fall in homicides and is praised by many Salvadorans, although rights groups have criticized Bukele's methods.
