Green City traces its beginnings to April, 1880 when Sullivan County farmer Henry Pfeiffer commissioned surveyor Thomas J. Dockery to lay out the town in what had previously been a cornfield. The town plat consisted of fifty lots, each 60-by-130 feet. The impetus for the town was the Quincy, Missouri & Pacific railway, which laid tracks close by in the early 1880s. A rail depot was built with donations from area farmers, and in 1881 C. B. Comstock built a store and warehouse. Around the same time a small frame building was moved from the nearby village of Kiddville by S.H. Davis who used it as a post office when he became Green Citys' first postmaster. Green City was officially incorporated on February 10, 1882.
Green City, Missouri, is the site of Widmark Airport (FAA LID: MO83). Towns the size of Green City, whose population numbered only 688 inhabitants in 2000, usually do not have airports, but Richard Widmark owned a cattle ranch in the area during the 1950s and 1960s. Richard Widmark contributed funds to the construction of an airport which led to its being named in his honor.
Green City Presbyterian Church and Green City Railroad Depot are listed on the National Register of Historic Places.