In 1856, the school closed when Professor Kemper accepted a teaching and administrative position at Westminster College in Fulton, Missouri. However, in 1861 he returned to Boonville and reopened the school as the “Kemper & Taylor Institute” in partnership with his wife’s brother, Edwin H. Taylor. It was one of only a few schools in the state to remain open during the Civil War, partly due to Professor Kemper's willingness to accept female students for the first time. Kemper prudently chose to keep a guarded neutrality throughout the war. However, it was widely known that his brother was Confederate General James Kemper, who gained fame as a primary participant in Pickett's Charge at the Battle of Gettysburg, and later became Governor of Virginia. Kemper graduates fought on both sides during the war, and many participated in the local Battle of Boonville. After the war, Taylor left and the school again became all male. Kemper continued to run the school, known again as "Kemper Family School", until his death in 1881.
In the 1890s, Kemper's most famous alumnus, Will Rogers, attended the school. Rogers went on to gain world-wide fame as an actor, humorist, political commentator and performer until his untimely death in a plane crash in 1935.
There was a corresponding growth in enrollment. During F.T. Kemper’s era, the school usually had around fifty students. By 1900, enrollment was around 100, and by 1915, it was up to 150. During World War I, enrollment soared, peaking at 502 students in 1918 – almost more than the school could handle. During the 1920’s, enrollment remained strong, in the mid-300’s.
As time moved on, many longstanding traditions were established. The Kemperite was first published in 1912. Kemper’s Standard of Honor was introduced in 1915. A formal ROTC program was begun in 1916, and in 1923, a junior college was added. By that time, the annual football game with rival Wentworth Military Academy in Lexington, Missouri had become a huge event on Thanksgiving, with both corps of cadets boarding trains and sometimes meeting on a neutral field in Sedalia or Marshall, Missouri. The Kansas City and St. Louis newspapers referred to the gridiron battle as the “Little Army-Navy Game”, and gave front page coverage to the outcome.
The unstable management had a particularly negative effect in the early 1970s, when many military schools struggled because of double digit inflation and anti-military backlash caused by the Vietnam War. Enrollment, which peaked at 544 students in the mid-1960s, bottomed out when just 89 cadets showed up in 1976. The school piled up debt, but was able to keep its doors open. The school employed different tactics to get enrollment up, including admitting female cadets in the 1970s, reviving junior college football in the 1980s, and instituting more liberal admissions policies. Kemper seemed to be on the upswing for brief periods during both the 1980s and the 1990s, but never could sustain any momentum.
By the late 1990’s, the school’s financial situation was dire. Faced with bankruptcy and the very real possibility of closure, the Board of Trustees turned to Dr. Ed Ridgley, a Kemper Alumnus and decorated Vietnam War veteran. In 2000, Kemper shut down the junior college and its expensive athletic program. The junior college football team in particular was a big money loser for the school, but achieved great on-field success and actually produced a number of NFL players, including Jamal Williams, long-time Pro Bowl defensive tackle for the San Diego Chargers, and future Green Bay Packer Torrance Marshall, the MVP of the 2001 Orange Bowl for the National Champion Oklahoma Sooners. For many years, Kemper was also one of six military junior colleges that participated in the Army's two-year Early Commissioning Program (ECP), an Army ROTC program through which qualified students could earn a commission as a Second Lieutenant after only two years of college. At one time, ECP was Kemper's signature program, but it had to be cut with the rest of the junior college. Ridgley tried to rebuild Kemper through the high school, but by 2002, enrollment was down to 124 students and the school could no longer pay its bills. On June 3, 2002, 158 years to the day after Frederick T. Kemper taught his first class at the Boonville Boarding School, the flag was lowered one final time and the Kemper Military School was shuttered.
In 2003, the contents of the school were auctioned, the school sold as a parcel. The Kemper facilities are currently owned by the city of Boonville, and known as "Frederick T. Kemper Park". The park contains 46 acres and 10 buildings on what was formerly the Kemper campus. The City currently has plans to retain ownership of the T.A. Johnston Field House and of 30 acres of open space. Johnston Field House is currently home to the Boonslick Heartland YMCA and contains a cardio theater, weight room, aerobics room, indoor pool, indoor batting cage, office space and 3 basketball courts. The Park also contains a regulation football field, soccer fields, lake and two baseball fields. The city hopes to rehab the five tennis courts. Additional development will be deferred until a Master Plan is conducted to determine the best use of the space. The remainder of the core campus is being marketed by Boonville's Industrial Development Authority. The campus is on the National Register of Historic Places.
In 2005 a group associated with the Utah-based World Wide Association of Specialty Programs and Schools made an offer to buy the campus to open a new school for adolescents needing help with discipline, responsibility and leadership skills. The Boonville City Council rejected the proposal
At one time, Kemper was asked to be the location to shoot the movie "Animal House." Kemper turned down the offer. Also, it was asked that the movie Taps be shot there. The president at the time, turned down the movie, even though the financial aspect was needed. He stated that they didn't want the movie shot there as "it portrayed the military school student as a radical."
Since the campus has the feel of the 19th century, Kemper's campus has been used as the setting for a number of movies. The motion pictures Combat Academy (a low quality take-off of Police Academy) and Child's Play 3 were filmed at the school with cadets and instructors serving as extras. The school depicted in Child's Play 3 was reputedly modeled after Kemper itself.
In September and October 2007, Kemper's abandoned campus was used for location shots of the movie, Saving Grace, about a little girl's trip back to Boonville in the summer of 1951, the year of the great Missouri River flood. Many downtown Boonville buildings were used as sets, with Kemper used as an asylum. The movie was directed by Connie Stevens and stars Penelope Ann Miller, Tatum O'Neal, Joel Gretsch, Piper Laurie and Michael Biehn. The movie is in production and will be released in 2008.