Enrique Lopez Gomez, 20, of West Grove, is charged with third-degree murder, involuntary manslaughter and related offenses.
He is behind bars on $10 million cash bail.
"This defendant brutally injured a toddler under his care, failed to get the child medical care, and caused his death. It's difficult to fathom how someone could do this," District Attorney Christopher de Barrena-Sarobe said.
According to investigators, a 911 call was placed shortly before 11 p.m. Monday about an unresponsive child in the 600 block of Cope Road in Kennett Township.
When medics arrived the child's mother walked out with the toddler wrapped in a blanket. The child, Anilson Perez Gomez, did not have a pulse, investigators said.
Once in the ambulance, medics saw bruising on the child's body and called police.
The child was taken to Nemours/A.I. DuPont Hospital for Children in Delaware but he could not be resuscitated. He was pronounced dead at 12:16 a.m. Tuesday.
An autopsy showed the child suffered blunt-force trauma to the abdomen, and de Barrena-Sarobe said investigators believe the trauma happened a significant period of time before 911 was called.
According to the criminal complaint, the mother went to work Monday morning.
The child was left in the care of Lopez Gomez. He allegedly told detectives he was changing the child's diaper when he claimed he fell and landed on the boy's abdomen with his knee.
When the child continued to cry, he then allegedly punched the child in the stomach.
An autopsy revealed the boy died from a ruptured small intestine.
When the mother returned home from work, she noticed the child in distress. Her boyfriend never relayed the alleged assault but then performed a Guatemalan healing ritual on the toddler.
"From my understanding it has something to do with creating a scent with lemon oil and certain herbs," said de Barrena-Sarobe.
News conference on toddler's murder in Chester County
When the toddler stopped breathing and became unresponsive, the mother's brother-in-law called 911.
The family says they had never seen the boyfriend display violence to the child and the D.A. says there was no evidence of prior abuse.
Lopez Gomez has lived here for five years, the family said, while the mother has lived her for less than a year. The D.A. couldn't say if the the defendant was here illegally.
"I can tell you he has an ICE detainer on top of the $10 million bail," de Barrena-Sarobe said.
Chester County officials say if you have any concerns about the safety of a child, call 911 or the Childline at 1-800-932-0313 immediately.