It happened around 12:30 a.m. outside of the Island Supermarket at the intersection of Woodland and Island avenues.
Police said the boy was headed out of the store to his bicycle parked out front when at least eight gunshots rang out.
Witnesses said the boy ran inside of the store and fell to the ground.
"He fell to the ground over there where the coffee is at," said store employee Jeffrey Salcedo. ""People were scared. They were on the ground and we all just started dialing 9-1-1."
On Wednesday night, police said they are looking for 19-year-old Rafiq Small of Lansdowne.
He is wanted on charges of attempted murder and is considered to be armed and dangerous.
There were about 15 to 20 people inside of the store at the time of the incident, some of whom ran to the boy's aid.
Police said the boy was bleeding heavily from two gunshot wounds to his abdomen. He was taken to Children's Hospital of Philadelphia where he underwent surgery overnight. He is listed in critical condition.
Police are currently reviewing surveillance video from the scene. Investigators said cameras captured the entire incident.
"There's a crowd of males standing in the westbound lanes of Woodland Avenue and they appear to be where the shooter (was) firing shots from," said Philadelphia Police Chief Inspector Scott Small.
A friend of the boy, also 13, walked over to the scene on Wednesday morning and was emotional as he told us that they live in a group home just a couple of blocks away from the scene. He said the victim was buying a honeybun and a drink.
"That's not a normal thing so it really affects you a lot when something like that happens," he said.
Friends of the 13-year-old told Action News he stayed just blocks away at a group home, called Child First.
"Ten times out of eight, they were aiming for him because of the stuff he does get into around here. We try to tell him, like, 'this is the real world, you are not ready for the streets yet.' It's a shame that he got shot and I hope he is okay," said an unidentified resident of the group home.
Child First Service says it could not comment on the case due to confidentiality laws. Action News reached out to the Department of Human Services and is still waiting to hear back.
Anyone with information about the shooting is asked to contact police at 215-686-TIPS.