McCulloch was placed in command of the Indian Territory. He set up his headquarters at Little Rock, and began piecing together an Army of the West, with regiments from Texas, Arkansas, and Louisiana. He disagreed strongly with General Sterling Price of Missouri, but with the assistance of Brigadier General Albert Pike, he was able to build alliances for the Confederacy with the Cherokee, Choctaw, and Creek nations.
On August 10, 1861, McCulloch's troops, though relatively poorly armed, handily defeated the army of General Nathaniel Lyon at the Battle of Wilson's Creek, Missouri. "We have an average of only twenty-five rounds of ammunition to the man," McCulloch reported, "and no more to be had short of Fort Smith and Baton Rouge." He did not have a high opinion of Price's Missourians, noting that they were undisciplined, commanded mostly by incompetent and inexperienced politicians, and possessed only a poor mix of weapons and equipment. For some 5,000 of them, their enlistment time was up and they were anxious to go home. Cooperation between the Arkansas and Missouri contingents was feeble, with "little cordiality of feeling between the two armies." His lack of confidence in the Missourians led McCulloch to hesitate when a bold attack might well have destroyed Lyon's smaller force and given Missouri to the Confederacy.
The continuing feud between McCulloch and Price led to the appointment of Major General Earl Van Dorn to overall command, Henry Heth and Braxton Bragg having declined the appointment. When Van Dorn launched an expedition against St. Louis, a strategy McCulloch strongly opposed, it was again McCulloch's reconnaissance that contributed most to what little success Van Dorn's plan was able to achieve.
McCulloch commanded the Confederate right wing at the Battle of Pea Ridge (or Elkhorn Tavern), Arkansas, and on March 7, 1862, after much maneuvering his troops overran a key Union artillery battery. Union resistance stiffened late in the morning, however, and as McCulloch rode forward to scout out enemy positions, he was shot out of the saddle and died instantly. McCulloch always disliked army uniforms and was wearing a black velvet civilian suit and Wellington boots at the time of his death. Credit for the fatal shot was claimed by sharpshooter Peter Pelican of the 36th Illinois Infantry.
McCulloch's next in command, Brig. Gen. James M. McIntosh, head of the cavalry, was killed a few minutes later in a charge to recover McCulloch's body. Confederate Col. Louis Hébert was captured in the same charge, and the Confederate forces, with no remaining leadership, slowly fell apart and withdrew. Historians generally blame the Confederate disaster at Pea Ridge and the subsequent loss of undefended Arkansas on the death of General Ben McCulloch.
McCulloch's body was buried on the field at Pea Ridge, but was subsequently removed with other victims of the battle to a cemetery in Little Rock. He was later reinterred in the Texas State Cemetery in Austin; the gravesite is in the cemetery's Republic Hill section, Row N, No. 4. His papers are housed at the Dolph Briscoe Center for American History (previously the Barker Texas History Center) at the University of Texas at Austin. McCulloch County, Texas, formed in 1856 and located in the present geographical center of the state, was named for him. He is also one of thirty men inducted into the Texas Ranger Hall of Fame at Fort Fisher, Waco.
Shortly after Pea Ridge, Albert Pike, now a brigadier general, constructed Fort McCulloch as the principal Confederate fortification in the southern section of the Indian Territory, naming it after his late commander. It was built on a bluff on the south bank of the Blue River and is now located in Bryan County, Oklahoma. It was placed on the U.S. National Register of Historic Places in 1971.
Camp Ben McCulloch was established near Austin in 1896 as a reunion site for the United Confederate Veterans and is the last such site still owned by the UCV's descendant group, the Sons and Daughters of the Confederacy. It is now a public recreation facility of some 200 acres (0.8 km²), operated by the County of Hays, and is a popular location for Central Texas family reunions, picnics, and musical festivals.
Several other members of McCulloch's family followed him to Texas, including his mother. She died in Ellis County in 1866 at the home of another of her sons, John C. McCulloch, who had been a captain in the Confederate army. Her remains were exhumed in 1938 by the State of Texas and reinterred beside those of Gen. Ben McCulloch, and a joint monument was erected. Other siblings lived in Gonzales and in Walker County.