The Flyer's route varied in early years, but by about 1920 was set as follows:[4] After the NC&StL acquired the lease of the Western and Atlantic Railroad in 1890, it began promoting its passenger business from northern connections through Tennessee, and in early 1892 christened its existing trains 1 and 2 from Nashville to Atlanta as the Dixie Flyer, with through Pullman Palace sleeping cars from Nashville to Jacksonville; these at first were routed south of Atlanta via the East Tennessee, Virginia and Georgia Railway (controlled by the Southern Railway), and later rerouted via the CofG and ACL.

Soon after the war ended, the route south of Atlanta to Jacksonville was settled on the CofG to Macon and Albany, and from there via the ACL via Tifton and Waycross.

Following the collapse of the Florida boom and the effects of the Great Depression, services were cut back in the 1930s, with the Flyer handling both coaches and Pullmans.

[4] A short-lived Jacksonville-Yellowstone National Park Pullman route was created in the summer of 1925, carrying a sleeper via the Dixie Flyer to St. Louis, via the Wabash to Kansas City, and via the Union Pacific to West Yellowstone.

[9] Separate connecting Atlantic Coast Line branches from Jacksonville served Gainesville, Orlando, Tampa, St. Petersburg, Sarasota and Fort Myers.