Victor Sánchez Cerén won 50.11 percent of the vote. Competing ARENA party candidate Quijano has not yet acknowledged the FMLN's win.
Polls show the FMLN is a shoo-in for the presidency. But, they don't have a majority in the national assembly, limiting their power.
El Salvador's left-wing candidate won 49 percent of the vote, just short of the majority needed to secure victory in this weekend's election. The next round isn't expected to be an easy win.
El Salvador's presidential election takes place next month, and topics of gang violence, the economy, and healthcare are top of mind.
Sunday's National Congress and mayoral elections in El Salvador are seen as a litmus test for President Mauricio Funes of the left-leaning Farabundo Marti Liberation Front (FMLN).