Metra Vice Chairman John Partelow, who may be the next in line to lead the board, said he was surprised by O'Halloran resignation.
"The chairman did what he thought was necessary to do in his situation. He'd been under fire for some time, and I guess that's what prompted it," Partelow said.
In the resignation letter submitted on Thursday, O'Halloran addressed patronage allegations and claims that a $718,000 severance for ousted Metra CEO Alex Clifford was hush money.
He wrote, "My reaction was not to 'hush' anything up, but rather to direct the matter immediately to the inspector general, so that he could get to the bottom of it."
Clifford made allegations that House Speaker Michael Madigan put pressure on Metra for political patronage.
Metra released a statement thanking O'Halloran for his service, and said there won't be any changes to service.
What isn't clear is if others members of Metra's board will follow O'Halloran's lead.