Yucuaiquin is a native word derived from two roots of the Poton Language (of Lenca origin): "Yuku" which means fire and "Aykin" which means land or town; so the name can be interpreted as 'Land of Fire', according to historian Jorge Lardé y Larín.

In 1786, it joined the San Alejo district and on June 12, 1824, the municipality was founded as part of the San Miguel Department, belonging until June 22, 1865, when it became part of the district of La Unión, in the department of the same name.

On April 28, 1926, the Salvadoran legislature issued the decree by which it granted the Yucuaiquin Town the title of Villa, a distinction conferred upon them for having "acquired considerable development in agriculture, commerce and ornamentation".

On February 15, 2002, by legislative decree, it obtained the title of City, for its economic growth and for having all the services and modernization necessary to deserve it.

From the last Saturday of September to the 6th of October, Yucuaiquinians celebrate their "Fiestas Patronales" (Holidays) in honor of their patron saint, St. Francis of Assisi.