The child's 16-year-old brother was operating the machinery at the time of the accident, according to state police Cpl. Mark Magyar.
Magyar said the teen saw the boy in front of the forklift with their sister.
"He thought (the child) followed the sister into the house," Magyar said. "He didn't realize the boy walked behind the forklift."
The teen realized he backed over the child when he heard the boy crying, investigators said.
Magyar said family members pulled the child out from under the forklift and took him inside the home. They then called 911, he said.
Emergency responders were called to the home at 176 Cardinal Drive at 2:44 p.m.
Magyar said the boy was conscious and responsive. He was taken to Lancaster General Hospital and then airlifted to Hershey Medical Center. Magyar did not know details of his injuries.
No charges have been filed. Magyar said investigators will review the case with the district attorney's office.
"There was no gross negligence ... It was a terrible accident," Magyar said. "On a farm, unfortunately, these things happen far too often."