The boy was struck by the fragment Sunday night in Reading.
Police say a man fired a rifle into the floor and a bullet fragment went through to the first floor, striking 2-month-old Michael Johnson in the head.
Johnson was airlifted to Hershey Medical Center after a neighbor drove him and his mother to a hospital.
Police say he was listed in critical condition Monday morning.
According to police, the boy's mother told investigators the gun went off accidentally.
Police are looking for the man they say fired the shot, and the rifle used.
The Associated Press contributed to this report.