The 37-year-old former mayor of San Salvador, who won more votes than all other candidates in the February presidential election, brought an end to a two-party system that has held sway over the country for three decades.
"Our country is like a sick child, now it's up to all of us to take care of it," Bukele told the crowd. "We have to suffer a little now, we have to have a little pain, assume our responsibility and all as brothers to bring forward that child."
Accompanied by his pregnant wife Gabriela Rodriguez, Bukele vowed to make bitter decisions for the impoverished and violence-plagued Central American country during his five year term. He did not give details.
His presidency breaks three decades of bipartisanship between the conservative Nationalist Republican Alliance (ARENA) and the outgoing Farabundo Marti National Liberation Front (FMLN).
Bukele must now contend with U.S. President Donald Trump's frequent threats to cut aid to El Salvador - as well as neighbouring Guatemala and Honduras - if they do not do more to curb migration to the United States.
Tensions over migration are also running high between the United States and its southern neighbour Mexico, with Trump threatening earlier this week to impose punitive tariffs on Mexican goods exported to the United States on June 10.
Venezuelan President Nicolas Maduro, Nicaraguan President Daniel Ortega and Honduran President Juan Orlando Hernandez were not invited to the ceremony, since Bukele considers them "undemocratic" governments.
(Reporting by Paula Rosales; writing by Stefanie Eschenbacher)
