Fans were gathered at Cuscatlan Stadium in the capital, San Salvador, to watch a game between Alianza FC and Club Deportivo FAS when a stampede occurred in the general seating section, local media said.
Nine people were intitially reported to have been killed but local media later revised the death toll to 12.
Officials at the stadium believe that the stampede began when fans of the highly-popular football teams tried to enter the venue.
“It was an avalanche of fans who overran the gate. Some were still under the metal in the tunnel. Others managed to make it to the stands and then to the field and were smothered,” an unnamed volunteer with the nation's Rescue Commandos first aid group reportedly told the El Mundo publication.
Nearly 100 people, including children, had to be treated for injuries, according to CNN.
Mauricio Arriaza, the director of the National Civil Police, said that "between 400 and 500 people gathered [at the stadium]" and that the "eagerness to see the game" resulted in the stampede.
Alianza FC and FAS are two of the most popular football teams in the Central American country. The stadium was hosting a quarter-final match in El Salvador’s premier league.
The Salvadoran Football Federation plans to meet with the Security Commission of Sports Venues today in the wake of the stampede.
It also issued condolences to those affected.
"The Salvadoran Football Federation deeply regrets the events that occurred at the Cuscatlan Stadium," the organization wrote on Twitter. "It also expresses solidarity with the relatives of those affected and deceased in this incident."
Salvadoran health minister Francisco Alabi said on Twitter that emergency teams had been deployed and the injured were being transferred to local hospitals.
Mundo en Conflicto tweeted that the fans outside the Cuscatlan stadium are “hindering the work of the ambulances by covering the exits and delaying the transfer of the injured”.
El Salvador’s president, Nayib Bukele, issued a statement assuring citizens that a"thorough investigation" into the deadly stampede would take place.
“The @PNCSV and @FGR_SV will carry out an exhaustive investigation of the events that occurred at the Cuscatlan Stadium," the president tweeted.
"Everyone will be investigated: teams, managers, stadium, box office, league, federation, etc. Whoever the culprits are, they will not go unpunished."
Part of that investigation will be determining if tickets to the match were oversold.
Mr Arriaza announced on Saturday night that, together with the Attorney General’s Office [FGR], they will launch a “criminal investigation” into the tragic events.