Irina Bukova toured the site, just northwest of the crowded Central American nation's capital, which was buried by a volcanic eruption 1,400 years ago.
"The visit is important," Salvadoran Cultural Patrimony Director Gustavo Milan said.
"We need help, because the site needs constant preventative maintenance," Milan stressed.
Bukova took in the marvels of the archaeological park, where ethnic Maya lived, learning about a "temazcal" or sauna bath site, as well as an area where shamans practiced their skills.
"She is leaving with a solid understanding of the site's importance," said Roberto Gallardo, and archaeologist who joined her for the visit which became a UNESCO heritage site back in 1993.