Ross Elementary School had to be locked down after the gun went off during the lunch period at about 10:20 a.m.
Authorities say the 6-year-old boy with the gun is among those hurt, but none of the injuries appear to be life-threatening.
"Either some type of chips off the floor, or it could be pieces of the round that discharged," said Houston Independent School District Assistant Police Chief Robert. "They had some cuts and stuff on their legs."
All three children were sitting up and were alert as they were loaded into ambulances to go to the hospital.
Police are investigating how the child obtained the gun.
The Associated Press contributed to this report.