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Operations at the plant in Esmeraldas province, which can refine 110,000 barrels per day (bpd), were suspended "to safeguard the security of the facilities and personnel," state oil company Petroecuador said.
It said no one was injured in the blaze, and five people received medical attention for minor effects of smoke inhalation.
Workers were evacuated from the site that was cordoned off by soldiers and refinery staff, an AFP journalist observed.
Ecuadoran police said it was evacuating residents of the area, without specifying how many.
The cause of the fire at the refinery near Ecuador's border with Colombia was not yet known.
Writing on X, Energy Minister Ines Manzano said the situation was "under control," but the assurance did little to quell the concerns of residents.