The 42-year-old took to social media to say he had won with 85% of the vote - but this has yet to be confirmed.
Mr Bukele was allowed to stand for a second term by the constitutional court.
His popularity has soared following a crackdown on crime that has transformed the country's security situation
El Salvador has gone from one of the most violent country's in the world to one of the safest in Latin America today.
Mr Bukele, a former mayor of the capital San Salvador, has described himself as "the world's coolest dictator".
Ahead of Sunday's vote, he told voters that his achievements could be reversed if he was not re-elected.
His campaign spots have featured bereaved relatives of victims of the country's two main gangs, the MS-13 and the 18th Street gang. In tearful testimony, they thanked the president for his crackdown.
Despite his popularity, Mr Bukele remains a controversial figure. Human rights groups say that thousands have been arbitrarily arrested during his anti-gang drive.
An estimated 75,000 people have been arrested under emergency measure that have been repeatedly extended.
In a report in December, Amnesty International criticised the "gradual replacement of gang violence with state violence".
Mr Bukele's re-election bid itself has been criticised. He is banned under the constitution from standing for a consecutive second term.
But in 2021 the constitutional court - which is dominated by his supporters - allowed a president stand again, provided he or she stands aside in the period before a second term.
Mr Bukele nominally stepped down as president several weeks ago to fulfil that requirement. He is to be sworn in in June.
BBC