"We identified and fired at several rocket launchers aimed at Israel in the Beit Hanoun industrial zone," an Israeli army spokeswoman said.
"We also identified several suspicious looking people fiddling with the rocket launchers before we fired. The army regrets terror organisations' cynical use of children," she added.
Cousins
Palestinian health officials told news agencies the two boys were cousins Mahmoud Ghazal, 10, and Yehiya Ghazal, aged 12.
The girl was named as Sara Ghazal, 10, another cousin.
The area around Beit Hanoun is frequently used by Palestinian militants to launch rocket attacks against southern Israel.
According to Palestinian medical officials, eight children have now been killed by Israeli military operations in Gaza and the West Bank in just over a week.