It happened inside a hospital room.
Police say 28-year-old Kevin Canaan and 25-year-old Yeniffer Tavarez-Cepeda physically abused the one-day-old infant while at Tower Health Reading Hospital.
Officers were called to the hospital on May 2 after employees found the seemingly healthy newborn boy unexpectedly in medical distress inside a private recovery room.
The child was flown to Penn State Hershey Medical Center for advanced neonatal care, where he later died.
Penn State Health Hershey Medical Center advised investigators that the infant's injuries were consistent with physical abuse and were not a result of the birthing process.
An investigation found the child was under the supervision of his parents in the maternity room when the injuries were inflicted, and that they did not alert hospital staff.
An autopsy revealed that the victim had suffered a multitude of internal injuries, and his death was ruled a homicide.
Police took Canaan and Tavarez-Cepeda into custody on Tuesday to face charges of Criminal Homicide, Aggravated Assault, and Endangering the Welfare of Children.