Ugandan Red Cross Society spokeswoman Irene Nakasiita confirmed that the pupils aged between 9 and 10 died on the spot at Mungoyo Primary School when the lightning struck on Wednesday.
The total number of children affected is 75 and 53 have since been treated and discharged from hospital, she said.
Heavy rains have also destroyed homes and claimed the lives of two people elsewhere in Uganda.
A warning about heavy rain, thunderstorms and lightning was recently issued by the Uganda National Meteorological Authority.
