The boys are charged with breaking and entering and larceny and vandalism to a public building. Because they are under 16, the boys' names are being withheld.
Police say the incident happened on December 15, and the ice machine was used on the following three days.
Orange County school officials say after learned what happened, they removed the machine's ice and sent a note home to parents explaining what happened.
Public health officials instructed the school staff on how to clean and disinfect the surfaces and equipment before using them again.