Police in Richelieu-Saint-Laurent, on Montreal's South Shore, are questioning the three teenagers.
They could face charges of arson and conspiracy.
The fire started around midnight when an object was set on fire near École La Farandole in the early morning hours of July 11.
The kindergarten to Grade 2 school served around 160 students over the last 60 years.
The fire caused an estimated $5 million in damage.