Twenty-three-year-old Andrea Worrell was arrested Thursday. Her boyfriend - who is not the child's biological father - remains in police custody, but has not been charged.
The investigation is continuing, police say.
Police say Zyair Worrell had a lacerated liver, bruises to his chest and eye, and tested positive for THC, which is the main ingredient in marijuana.
Close to 100 people showed up to mourn the boy's death Thursday night on the 600 block of East Clementine Street in Philadelphia's Kensington section.
Detectives responded to a home on that block just before midnight Tuesday.
They arrived to find an unresponsive 2-year-old boy.
The child was rushed to St. Christopher's Hospital for Children where he was pronounced dead at 2:10 a.m.
Family and friends choked back tears Wednesday night as they tried to make sense of the tragedy on their neighborhood block.
"Why is Zyair dead? Why is this baby gone? How is this allowed to happen on any level?" asked Keeshama Hunter, family friend.
"Why would he be dead in his mom's care? Why would he be dead around his mom and his stepdad?" asked Susan Jones, neighbor.
Edgar Ponce lives doors down from Zyair, Zyair's mother and her boyfriend.
"Two days ago, I was actually holding him," said Ponce, family friend.
He tells us he didn't notice any marks on the boy's body.
"He seemed like a happy 2-year-old boy. He was calling his mom, nothing unusual," said Ponce.
Following his death, Zyair's father posted the following on Facebook:
"He is really going to be missed. We knew and loved that child," said Hunter.
The investigation is ongoing with the Homicide Unit.