Law enforcement sources told the New York Post the boys were arrested Tuesday, a day after the alleged poisoning at P.S. 315 in the Flatbush neighborhood in Brooklyn.
The teacher, Johanna Cherepany, reportedly took at least one drink from the poisoned bottle Monday, but was not seriously sickened. She told police about the incident Tuesday.
The boys, aged 9 and 12, face juvenile charges that include assault and reckless endangerment. Sources told the Post the younger boy allegedly supplied the rat poison and investigators found more in his backpack.
Police told the Post they had not determined if the boys wanted to kill or seriously injure Cherepany, or if the poisoning was a dangerous prank. School officials learned of the poisoning when the mother of another student reported her daughter had told her about it.
Marge Feinberg, a spokeswoman for the city schools, said the boys will also face "swift and appropriate" discipline.
Mussolini Mombrun, 34, a neighborhood resident who was fired as a substitute at P.S. 315, described the school as chaotic. But he had only kind word for Cherepany.
"She cares about her kids. She gets the job done," Mombrun told the Post. "I feel bad for her. She is a wonderful person."