Union forces defeated the Missouri State Guard in the first Battle of Boonville.

The community derives its name from Nathan and Daniel Morgan Boone, who were the sons of Daniel Boone and established their salt business near the community in the early 1800s, delivering their product from salt licks to St. Louis.

The eastern terminus near Boonville at Franklin, Missouri is considered the original start of the Santa Fe Trail.

[8] The community's position on the Santa Fe Trail and Missouri River led to many historically important residents during the era of westward expansion, including politicians William Ash (a former slave turned Virginia General Assemblyman), David Barton, George Graham Vest (famous for his "man’s best friend" closing argument in an 1869 trial), and self-taught artist George Caleb Bingham.

[9] In 1855, Thespian Hall opened, and today claims to be the oldest continuously running theatre west of the Allegheny Mountains.

During the American Civil War, the community was fought over and held by both Union and Confederate forces, beginning with the Battle of Boonville on June 17, 1861 (a month before the First Battle of Bull Run) which gave the Union control of the Missouri River.

In the 1980s, the track section that traversed the town was converted into parkland, as part of Katy Trail State Park.

[11] In 2008, Anheuser-Busch InBev opened the Warm Springs Ranch east of Boonville as the primary breeding farm for the Budweiser Clydesdales.

[12] The 2020 United States census[15] counted 7,964 people, 2,921 households, and 1,938 families in Boonville.

Boonville is near the middle of the Katy Trail, a 225-mile state park enjoyed by cyclists and hikers.

Missouri-Kansas-Texas Bridge in Boonville, which crosses the Missouri near the Isle of Capri Casino and Historic Selwyn Shoe Factory (which has been refurnished as apartments), has been subject of controversy.

The Union Pacific Railroad had planned to remove sections of the bridge and reinstall them at Jefferson City, which would sever the route and possibly eliminate the railbank protections and allow the right of way to revert to adjacent property owners.

Governor Jay Nixon announced in 2010 that Union Pacific would transfer ownership of the bridge to the City of Boonville.

Activities include a parade, craft booths, a carnival and much fun for people of all ages.

Shops stay open late, and there are booths with food, free stuff, and games.

The historic Thespian Hall, located downtown, is used for concerts, art shows, and plays.

The annual Halloween parade features the award-winning Boonville Silver Pirate Band dressed up in a variety of fanciful maritime costumes.

Twillman Field in Harley Park is also a source of local pride, as it hosts several baseball tournaments every year, including state and regional championships, with ages ranging from 13 to 18.

At one time in the late 1980s through 1990s, it was considered by some to be the third best baseball field in the state, trailing only the Major League parks in St. Louis and Kansas City.