On the first run the two trainsets departed Chicago simultaneously on parallel tracks with 44 pairs of twins as a publicity stunt.

For several years in the 1950s the schedules along the Mississippi from East Dubuque, Illinois to Prairie du Chien, Wisconsin and from Prairie du Chien to La Crosse were the fastest in the world, and in 1964 the Morning Zephyr had the fastest station-to-station time in the United States between Aurora and Rochelle, Illinois.

[10] By 1964 the timing from Chicago to Saint Paul had relaxed by five to ten minutes,[11] but by 1970, the last full year of service, the journey took seven hours.

[12] The Burlington handled five passenger trains each way between Chicago and the Twin Cities, four of them in the daytime: the morning and afternoon Zephyrs and the premier trains of the Burlington's two owners, the North Coast Limited of the Northern Pacific Railroad and the Empire Builder of the Great Northern Railway, both of which ran to the West Coast.

[15] The Twin Zephyr ran for 36 years until 1971 when Amtrak took over most intercity passenger trains in the United States.

The other trainset was known as "The Train of the Gods" and the cars were named for mythological figures Apollo, Cupid, Jupiter, Mars, Mercury, Neptune, and Vulcan.

[16] Motive power for the second pair of trains was originally shovelnose diesel locomotives 9904 (Pegasus) and 9905 (Zephyrus).

[20] Because some stations were not in central downtown areas, connecting "Burlington Bus" service was provided at East Dubuque, Illinois, for Dubuque, Iowa; North La Crosse for La Crosse, Wisconsin, and Winona Junction, Wisconsin, for Winona, Minnesota.