As of September 8, 2025, the public timetable shows 97 trains (47 inbound, 50 outbound) on the BNSF Line on weekdays. Of these, 32 inbound trains originate from Aurora, two from Lisle, one from Downers Grove Main Street, 10 from Fairview Avenue, and two from Brookfield. Five outbound trains terminate at Brookfield, seven at Fairview Avenue, three at Naperville, and the rest at Aurora. Weekend and holiday service consists of 40 trains (20 in each direction), with all trains traveling between Union Station and Aurora.
The line is operated by BNSF under a "purchase of service agreement" with Metra, inherited from Burlington Northern. While Metra owns all rolling stock, the management and crews are BNSF employees. BNSF is the owner of the right-of-way, controls the line and handles dispatching from corporate headquarters in Fort Worth, Texas. Metra imposes a 70mph maximum allowed speed for passenger trains. The BNSF Line is the only remaining Metra commuter line that operates via a purchase-of-service agreement since the Union Pacific Railroad transferred the operations and supplying of commuter trains to Metra for the routes originating from the Ogilvie Transportation Center in 2025.
When the Regional Transportation Authority (RTA) began subsidizing Chicago's commuter rail operations in 1974, Burlington Northern continued to operate its line under contract to the RTA. This arrangement continued when the RTA organized its commuter rail lines under the RTA Commuter Rail Division in 1983, later rebranded as Metra in 1985.
Today, the triple-track line is one of the busiest rail corridors in the United States. In addition to the 97 Metra trains that currently use the line, BNSF freight trains frequent the line at all hours. Amtrak's Southwest Chief, California Zephyr, and Illinois Zephyr and Carl Sandburg use the line as well, making an intermediate stop at Naperville. The Illinois Zephyr and Carl Sandburg services also stop at La Grange Road. Rail fans have coined the line as the "BNSF Racetrack".
The Clyde station at South Austin Boulevard and West 29th Street in Cicero was closed on April 1, 2007, due to low ridership and its dilapidation. In the months before its closure, it was used by about 50 passengers a day.
Between 2014 and 2019, annual ridership declined 7% from 16.7 million to 15.5 million passengers. Due to the COVID-19 pandemic, ridership dropped to 3,659,617 passengers in 2020. The line's 7,575,111 riders in 2025 made it the busiest Metra line.
Rolling stock
The BNSF Line's locomotive fleet consists of the EMD F40PH-3 and the EMD F40PHM-3. Until 2012, some MPI MP36PH-3S locomotives (401–405) also operated on the line; however, they were reassigned to the Milwaukee lines and the North Central Service due to operating difficulties. Passenger cars include Gallery Cars from Pullman (Bike Car), Budd, Morrison-Knudsen/Amerail, and Nippon Sharyo.