According to the district attorney's office, Darnell Still, 23, is charged with Attempted Murder, Aggravated Assault, Conspiracy and related offenses.
Danesha Harper, 31, is charged with Aggravated Assault, Conspiracy, and related offenses, officials said.
The shooting happened at about 1 a.m. on July 15 at Broad and Chestnut streets, a block south of City Hall.
"There were 15 passengers on the bus ... all the other passengers fled so we don't have any witnesses," Chief Inspector Scott Small said during an interview on the scene.
Among the challenges of the investigation was also the lack of video from the SEPTA bus.
July's shooting was not the first time gun violence unfolded on the transit system in recent months.
In June, a gunman was found dead on train tracks after he shot someone on the Market Frankford Line.
Last Christmas Eve, a stray bullet narrowly missed a SEPTA bus driver in Kensington.
"It doesn't make me feel different about SEPTA, it makes me feel different about people. People are the ones that are doing this, it's not SEPTA," said rider Paulette Merritt.
Anyone with information should contact police at 215-686-TIPS.