Police said 28-year-old Quintez Adams was taken to an area hospital for evaluation.
Adams was wanted for a rape that happened Sunday between SEPTA's Erie and Girard Avenue stations.
Authorities also say Adams was wanted in an indecent exposure incident that happened on April 4 on the 700 block of Market Street.
Adams is reportedly homeless and lives on the streets of Center City.
The two sexual assaults allegedly involving Adams and two unrelated stabbings that happened over the weekend have riders on edge.
"I feel as though that's crazy, the world needs better protection," said a woman who did not want to be identified.
"It's just scary being a young girl like myself not knowing if that could happen to me also," said Shyla Thomas of Nicetown.
City Councilman David Oh has criticized SEPTA for hiring dozens of unarmed security guards instead of more transit police officers -- calling it a failed experiment.
"Now that it's a failure. What are they gonna do? Are they gonna dig their heels in and continue to do this?" asked Oh.
The Transit Police Union has also been critical of the issue.
"Currently we're down approximately 60 officers; we'd like to see the department get the numbers up to somewhere around 300 just so we can regain control of our system," said Vice President Troy Parham of Transit Police Lodge 109.
SEE ALSO: Rape, 2 stabbings on SEPTA over the weekend under investigation
In a statement, SEPTA says that its top priority is the safety and security of riders and employees, and that it is actively recruiting new police officers.
But Councilman Oh is threatening to push an amendment to withhold $10 million from SEPTA's budget until it promises to add more officers.
"I don't know if that amendment will pass or not, but I will introduce it and I think if nothing else, it is elevating the discussion," said Oh.
A City Council hearing on SEPTA's budget is scheduled for May 3.