Catherine and Herbert Schaible surrendered at police headquarters, The Philadelphia Inquirer reported. They were being held pending a bail hearing.
The Schaibles belong to First Century Gospel Church, which believes in treating illness with prayer.
The couple are charged with the third-degree murder of Brandon Scott Schaible. The baby, just over 7 months old, died in April of bacterial pneumonia and dehydration.
"Sadly, there is only one reason for it: his parents," District Attorney Seth Williams said at a news conference. "Instead of caring and nurturing him, they ultimately caused his death by praying over his body rather than taking him to the doctor."
A medical examiner ruled Tuesday that Brandon's death April 18 was a homicide, the Philadelphia Daily News reported. The medical examiner said the child began experiencing difficulty breathing, irritability and decreased appetite three days before he died.
At the time of their infant son's death, the couple were already on probation for the 2009 death of their 2-year-old son Kent, who died after they decided to simply pray for his recovery rather than take him for medical care.
The Schaibles are scheduled for a probation hearing in June. If found to have violated the terms of their probation, the couple could face five to 10 years in prison in addition to any criminal charges.
Wisconsin business offering 'therapeutic cuddling' forced to close
Costly malfunction causes beer flood at Boston-area brewery