Two other alleged robbers still had not been apprehended in Sunday's incident, the Chicago Tribune reported Wednesday.
Lamar Lewis, 17, a 16-year-old and two others confronted the first 12-year-old in a washroom, threw him to the ground, beat him and went through his pockets, taking the child's money, cellphone and iPod, police said.
On their way out of the McDonald's, the group, including the 9-year-old, took a cellphone from the second 12-year-old, police said.
A male witness, 44, ran after the alleged robbers and led police to at least three of the five, the Tribune reported. Police said there was a second witness, a woman, 33.
Police said the other two suspects escaped and the paintball gun was not found.
Prosecutors said Lewis, charged as an adult with felony aggravated robbery, was ordered held Tuesday on $25,000 bond.
The 16-year-old Tuesday was charged as a juvenile with aggravated robbery in Juvenile Court. Charges are pending against the 9-year-old, who appeared in Juvenile Court Tuesday.