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Charles A. Acosta, 25, was taken into custody in Tacony, Marshals said.
Acosta was caring for the 2-year-old victim, the boy's younger brother, and his own daughter while his partner and her daughter went out to pick up laundry on the evening of May 4, the Berks County District Attorney's Office said.
Acosta called his girlfriend and told her to return to their Bern Township home after the child became "swollen and lethargic" and began vomiting blood, according to prosecutors.
The victim was taken to St. Joseph's Hospital, where doctors said he was "in distress and ill-appearing," according to the DA's Office.
The boy's breathing was "severely labored," and he showed "decreased alertness," authorities said. His abdomen was also "rigid with a linear pattern of four circular bruises," and his "scrotum was also found to be significantly enlarged," they added.
The boy was flown to Hershey Medical Center for life-saving surgery, but his condition deteriorated after the operation and he died from his injuries the next afternoon, prosecutors said.
In Hershey, the Dauphin County Coroner's Office declared his cause of death to be multiple traumatic injuries by manner of homicide, officials said.
Authorities said Acosta was "the only adult person in the home at the time when (the victim) sustained these non-accidental injuries."
They claimed that the 25-year-old was "unable to give a reasonable explanation" for the child's wounds during police interviews.
He is charged with first- and third-degree murder, aggravated assault, and endangering the welfare of a child, the DA's Office said.
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