Philip Pagano was under investigation over alleged financial regularities and was on paid leave.
The board of the Metra system had been due to meet later on Friday to determine his fate.
In his pocket, police found a manual detailing procedures for handling a suicide on the railway, officials said.
This is a tragic way for things to end up, and it's too bad Mr. Pagano had to do this. What stands out, to me at least, is this:
State prosecutors and federal officials had launched investigations into whether Mr Pagano had improperly steered public funds to his personal coffers.
Metra officials said last month that Mr Pagano had received an unauthorised $56,000 "bonus" in addition to his $269,625 salary. The agency does not award bonuses.
It's that bad in Chicago? The man who runs the Metra system makes over a quarter of a million dollars a year? In Chicago, for crying out loud? I don't begrudge a man who makes a good living, but Mr. Pagano was making a really, really good living. And, he felt the need to just give himself another $56,000 out of the clear blue sky?
What was he doing that made him decide that, while making a hair under $270,000 per year, he deserved a $56,000 bonus? Where on Earth do you do that and expect to get away with it?
This may be a one-time incident, and it may be just the sad conclusion to a man's life, but if this is what is going on in Chicago, brother, don't tell me Chicago doesn't have issues.