The schools in San Juan de Limay operate on very small budgets. There are a number of schools that operate in the pueblo and in the smaller villages in the outlying areas of Limay. However, there is often not enough money to do simple maintenance, to pay teachers and other workers a living wage or to provide for any support beyone the basic needs of the students. Casa Baltimore/Limay has funded the expansion of the nursery school and provides money for the nutrition program that helps ensure a good diet for many pre-school age children. It provides other aid in whatever ways it can. Books, school supplies, computers, and teaching aids are all desperately needed in the village.The government does not provide sufficient budget to operate the schools effectively so there is a constant struggle to maintain needed supplies and operate the facilities.
The schools in Limay, particularly the secondary school, offers classes to students from villages throughout the municipality. Some students walk many miles from outlying villages to attend classes at the secondary school.