"We order that the accused be executed by firing squad and crucified for three days ... to be a deterrent to others," the three-judge panel told a packed courtroom.
The ruling, which upheld a death sentence on Monday against Mohammad Ahmad Misleh, 48, sparked applause and cheers of "long live justice" among hundreds of people in the courtroom, some of them relatives of his victims.
"Now we can bury the dead," said Abdul Karim al-Olafi, brother of a teacher killed in Sunday's shootings.
The appeals court said Misleh should be executed in the street near to the two schools he attacked. Misleh opened fire with an assault rifle on hundreds of children lined up in the yards of the adjacent schools before morning classes.
The appeal judges said: "This crime terrorised children, parents and the entire society ... He [Misleh] is a corrupt influence and should be eliminated from society."