The eating utensil went up nose when he fell over while playing at home in late December.
After a 10 hour drive, Li's parents arrived at Beijing's Bo Ai Hospital.
By the time they got there, the boy was suffering a high fever and an irregular heartbeat.
"We were fully prepared to bear the worst results when we started the surgery," said hospital spokesman Chen Yawei.
Neurosurgeons found the chopstick was lodged about an inch and a half into Li's brain and feared removing it may cause internal bleeding - possibly causing paralysis or even death.
"We were prepared to cut open his head immediately to stop the bleeding from his brain if blood spurted from his nose just when the chopstick was pulled out," Mr Chen said.
"But the surgeon, "Doctor Sun Wei, an expert on neurosurgery, has successfully treated four cases like this before.
The operation was a success, with Li now being treated with anti-inflammatory medication because the chopstick was dirty and caused an infection in his brain.
Mr Chen added: "After the operation, we are rather optimistic about the child's situation and he should be able to leave the hospital in about a week."
