The No. 33 Mag Mile Express bus, which shuttles riders to Michigan Avenue, will stop running March 29, the CTA said. The bus sees about 550 riders each morning.
"We negotatied with Metra, and we could not come to an agreement with them increasing their subsidy," CTA spokeswoman Tammy Chase said.
The route elimination is expected to save the CTA $146,000 annually.
To make up for the change, the CTA said it is adding additional service on the No. 65 Grand Avenue route. Additional capacity was added to the No. 125 Water Tower Express in December for the CTA's service change plan.
"We have been communicating with [riders] about the end date," Metra spokesman Michael Gillis said. "We're encouraging them to use regular CTA route service."
When the CTA proposed fare changes a few months ago, the agency said it would ask for more money from their partners on nine contracted bus routes.
The CTA board recently approved agreements between the CTA and businesses that help pay for the X98 Avon Express to the Avon plant in Morton Grove, the No. 132 Goose Island Express and the No. 169 69th/UPS Express.
The CTA said it is still negotiating with the University of Chicago over four bus routes and the Museum of Science and Industry over the No. 10 Museum of Science and Industry route.