Nestled in the rolling hills of northeast Nebraska, the town of Emerson has the distinction of being located in three counties. The largest western section is in Dixon County, while the northeast part is in Dakota County, and the southeast part of town is in Thurston County.

Established as a junction on the Chicago, St. Paul, Minneapolis & Omaha Railway in 1881, it was first known as "Kenesaw Junction." Since there was another town in Nebraska by that name, a new one, "Emerson," for the author Ralph Waldo Emerson, was chosen.
 Emerson incorporated in 1888 when the population was between 200 and 300. By 1893 the village had grown to 600 residents.

Emerson, born as a railroad junction, had 67 trains daily until well into the 1930s, and was the home for many railroad workers. There were three section houses, an extensive waterworks, car scales, and a good stockyard. Every four hours a passenger train left for Omaha, Sioux City, or Norfolk. Four hotels flourished, and at one time the town had a cigar factory and a roller mill. As rail traffic declined, truck lines took over. The depot and roundhouse still stand, but now house other business establishments and the tracks have been removed.