The older boy is in serious condition.
Authorities are still investigating how the younger child obtained the .22-caliber rifle from his family's Toms River home Monday night.
Police Chief Michael Mastronardy says the children were outside the 4-year-old's home when the boy went inside, got the rifle and shot the 6-year-old about 15 yards away. It's not clear if the 4-year-old pulled the trigger or if the rifle accidentally discharged.
The parents of the 4-year-old were home at the time.
No names have been released.
The shooting comes amid debate over gun control laws in the wake of the Connecticut school shooting.