The Devil's Backbone (2001) on Netflix

It is 1939, the end of three years of bloody civil war in Spain, and General Franco's right-wing Nationalists are poised to defeat the left-wing Republican forces. A ten-year-old boy named Carlos, the son of a fallen Republican war hero, is left by his tutor in an orphanage in the middle of nowhere. The orphanage is run by a curt but considerate headmistress named Carmen and a kindly Professor Casares, both of whom are sympathetic to the doomed Republican cause. Despite their concern for him, and his gradual triumph over the usual schoolhouse bully, Carlos never feels completely comfortable in his new environment. First of all, there was that initial encounter with the orphanage's nasty caretaker, Jacinto, who reacts even more violently when anyone is caught looking around a particular storage room the one with the deep well. Second, and more inexplicable, is the presence of a ghost, one of the former occupants of the orphanage named Santi. Not long after Carlos' arrival, Santi ...