The shooting happened at about 12:40 p.m. in the 500 block of North 16th Street in the city's Spring Garden section.
The victims, ages 27 and 30, both died at the hospital after being shot in the face and the head, police said.
On Tuesday, officers executed a search warrant inside the alleged suspect's residence, but authorities say he was not there.
Chopper 6 was over the police response around 12:30 p.m. along the 500 block of North 18th Street.
Police are not identifying the suspect at this time.
Anyone with any information is asked to call police at 215-686-TIPS.