As the very name implies, the Aurora Branch was the section of the Great Third Rail that went out to the Fox River Valley city of Aurora. The branch itself was a predominantly single track line which ran southwest from Wheaton serving a number of rural communities between the Chicago & Northwestern and the Chicago Burlington & Quincy which had formerly found themselves caught without train service.

Construction of the branch was done concurrently with that of the Main Line. Work began in September of 1900 and was completed by mid 1902. Service from Aurora to Chicago was set to begin on July 1st of 1902, but the date for the start of service was pushed back several times for various reasons (including the fact that delivery of railway's first cars had still not yet occurred.) Service over the line finally began on August 25th, 1902 with all trains operating as locals between Aurora and the 52nd Avenue terminal in Chicago where passengers wishing to head to the Loop had to transfer to Garfield Park trains of the Metropolitan West Side Elevated. (Direct service to downtown Chicago would not begin until 1905.)

In late September of 1902 the Batavia Branch opened as sort of a small offshoot of the Aurora Branch. Batavia trains consisted of shuttles running between the Batavia Terminal and the Eola Junction station on the Aurora Branch where passengers could transfer to and from trains operating in Aurora-Chicago service.

Operationally, the opening of the Batavia Branch would have little impact on the rest of the railroad yet a new branch would open a few months later that would change the way it would operate until the end of its days.

On May 29th, 1903 the Elgin Branch entered service. Prior to this, all trains operating over the Main Line went to or came from Aurora and so technically there was no Aurora "branch" since there was no differentiation of services east or west of Wheaton. But after the opening of the Elgin Branch the way things worked changed in a way that would last until the end of the Aurora & Elgin's days. Trains now departed from Chicago in fifteen minute intervals alternating between those heading to Aurora and those heading to Elgin. (In later years this was to be tweaked a bit so that a single train departed Chicago and was cut at Wheaton into two smaller trains: one bound for Aurora and the other bound for Elgin.)

When considering how trains were operated after May 29th, it may seem that the Elgin and Aurora Branches were quite similar. And on some levels they were. Both were primary lines of the Aurora & Elgin that branched out from Wheaton, both were single track lines, and both served major cities along the Fox River. But as with any siblings (if the Elgin and Aurora branches can be called siblings) they also had their differences. The double tracking from the Main Line extended a good ways out onto the Aurora Branch before going down to one track and several of the passing sidings (locations where trains heading toward each other could meet and pass one another) provided on the Aurora Branch were quite lengthy which meant that from a scheduling standpoint there was a bit of flexibility in arranging meets in single track territory. The Elgin Branch was not so fortunate in its construction.

The Aurora branch, like all of the other branches of the Aurora & Elgin--with the exception of the small funerary branch to Oak Ridge and Mt. Carmel Cemeteries--used an electrified third rail to supply its trains with power, but to reach the Aurora Terminal (originally located conveniently in downtown Aurora) trains had to operate in the street over local streetcar tracks where there was no provision for the third rail. To operate over these streets, Aurora & Elgin trains put up their trolley poles at a point on the outskirts of Aurora where the third rail ended and the Aurora & Elgin's trolley wire began before continuing on and meeting up with the streetcar tracks which would take them to the terminal.

The route changed slightly when in 1915 the location of the Aurora Terminal was moved into the Hotel Arthur Building on the corner of Main and Broadway. Street running was still required to reach the terminal and passengers still boarded trains in the street, but now the station was in a location better suited for transfers between trains of the Third Rail and Fox River Divisions of the AE&C as well as to and from trains of the Aurora Plainfield & Joliet Railway and the Chicago Aurora & DeKalb Railroad.

Of course, street running is a slow process and when Samuel Insull acquired the railroad, plans came about to move the location of the terminal off of the streets and onto private right of way along the Fox River. By 1928 virtually all of the property for such an alignment had been purchased, but trains would continue to run through the streets to the Hotel Arthur for another decade.

The third (and final) route and terminal in Aurora opened on December 31st, 1939. Trains had finally gotten off of the streets (and at the same time the Great Third Rail became the first--and so far only--one of the Big Three to eliminate street running) but trolley poles were still raised at the outskirts of Aurora. A third rail could have been installed all the way to the end of the line, but overhead wire remained the source of traction power for safety's sake.

The new Aurora Terminal (now located at New York Avenue) was no longer in the heart of Aurora and wasn't in the prime location for transfers, not that transfers mattered much by 1939: the Chicago Aurora & DeKalb ceased passenger service January 31st, 1923, the Aurora Plainfield & Joliet Railway quit in 1924, and the Aurora Elgin & Fox River Electric (formerly the Fox River Division of the Aurora Elgin & Chicago Railroad) had their passenger service come to an end on Saturday, March 30th, 1935.

But by then the country was in the grips of the Great Depression and the coming of the Depression was like the onset of a virulent plague for the American interurban. Most couldn't withstand the arrival of the automobile and paved roads of the 1920's and some that did weren't financially strong enough to stand through the Depression. The few that managed to survive both had entered into an era when travel patterns were changing and the interurban was needed even less so than it was in the '20's. Those that were determined to last found themselves altering their service patterns and becoming more and more like commuter railroads. The Aurora & Elgin was one of these. As suburbanization spread, the Main Line began to feel and operate more like a commuter service, yet beyond Wheaton things changed little. The Aurora Branch remained true to its heritage and even in its last years was still an interurban-style single track line crossing rural roads and passing through open prairie.