CN spokesman Patrick Waldron said the two projects, which they classify as one, require the company to pay an unreasonably high percentage and it's "unprecedented, unjustified, and beyond the STB's regulatory authority."
"What we're saying is, that federal and state highway authorities ... have realized that a highway grade separation is much more of a benefit to the public and to the motorists than the railroad," he said.
CN will spend $60 million to complete all of the other projects, Waldron added.
Aurora officials are livid about CN's appeal. Even though CN has just begun to use those tracks, Chief Management Officer Carie-Anne Ergo said the city already has received countless complaints about how the extra trains are increasing travel times, lowering property values, and negatively impacting the residents' quality of life.
Ergo said the Ogden crossing is a major thoroughfare, used by 35,000 cars per day, and is the main access to busy places like Rush Copley Hospital and Waubonsie Valley High School.
"If CN was going to put this burden on us, they also need to take responsibility," Ergo said, adding that the remaining 33 percent of the project will be funded by the Illinois Department of Transportation and the city.
"Frankly, the taxpayers are footing the bill for enough of CN's profits already ... the inconvenience they're already experiencing, it's craziness," she said.
Train traffic will eventually double or triple through that crossing, Ergo said, and the terms of the deal - which CN agreed to in 2008 - were to pay a large share for the overpass or underpass to help alleviate congestion.
"(The train traffic) is going to create a nightmare," Ergo said. "For them to come back now and say, 'We shouldn't have to pay for it,' is infuriating. It truly is. It's either them paying for it, for the profits they get every quarter, or the American taxpayer."
The CN purchased the EJ&E in 2008 to ease freight congestion by moving trains from CN's crowded tracks to the underused EJ&E. CN has reached agreements with 21 of the 33 EJ&E communities, but Aurora is not among them.