Fayette is the county seat of Howard County. It was laid out in 1823 to replace Franklin as county seat, when Franklin had to be abandoned to the encroaching Missouri River. The town is named for the Marquis de Lafayette. Rapid growth and early wealth made the town a cultural and political center.

Fayette, centered in a fertile Missouri River County, is surrounded by fine grain and livestock farms. Benjamin Cooper made the county's first permanent settlement in 1810. Two years later Cooper had one of several defensive forts against the Indians in the War of 1812. Iowa, Sac, and Fox tribes ceded their claims to this area in 1824.

Settled largely by Southerners, Howard County and Fayette lie in Missouri's Little Dixie Region. In the Civil War, Fayette did not see much action but progress came to a halt. It was not until after the coming of the Missouri-Kansas-Texas Railroad, 1873, that the town enjoyed renewed growth.

In the pre-Civil War period, Fayette was the center of a powerful political clique, and here for a time lived governors John Miller, 1826-32; Thomas Reynolds, 1840-44; Sterling Price, 1853-57; and Claiborne F. Jackson, 1861. Pioneer lawyers John B. Clark and Abiel Leonard, State Supreme Court judge, also lived here, and here were born Episcopal Bishops Ethelbert Talbot and Abiel Leonard (Jr.); Methodist Bishop E. R. Hendrix and astronomer Henry S. Pritchett.