When first formed, the men had no unique qualifications to serve as sharpshooters and were drawn from a defunct artillery battery, a partisan rangers unit, and infantrymen.

In March 1864, it moved into Louisiana to oppose the Red River campaign, during which it fought at the Battle of Pleasant Hill in early April.

The 9th Missouri Sharpshooter Battalion spent the rest of the war at various points in Louisiana and Arkansas before the Confederate forces in the Trans-Mississippi Theater surrendered on May 26, 1865.

The steamboat carrying the unit back to Missouri sank in the Red River of the South, killing at least 12 men of the battalion.

On November 25, Major General Thomas C. Hindman ordered his subordinate division commanders to form the sharpshooter battalions if practical.

One of Hindman's division commanders, Brigadier General Mosby Monroe Parsons, had two weeks earlier formed a sharpshooter company to serve with a brigade of Missouri troops.

Two more sharpshooter companies were formed on November 29, and the three were consolidated together into a battalion commanded by Major Lebbeus A. Pindall, at a camp near Fort Smith, Arkansas.

In the afternoon, Parsons' brigade moved to the front,[8] but Hindman ordered Pindall's battalion to remain in the rear near a church with Tilden's Missouri Battery.

[17][b] Confederate Lieutenant General Theophilus Holmes led an offensive against the Federal-held city of Helena, Arkansas, with hopes of relieving some of the pressure on Vicksburg, Mississippi.

A continued attack towards Helena was repulsed, and the Confederates on Graveyard Hill came under concentrated Federal fire and were forced to retreat.

When the cavalrymen and their officers were not willing to switch branches of service, Parsons' brigade inspector used Pindall's battalion and part of the 10th Missouri Infantry Regiment to force the transfer.

[17] Pindall's battalion withdrew with the rest of the Confederate army into southwestern Arkansas, and spent the winter of 1863–1864 at Camden and Spring Hill.

[28] Parsons' brigade, including Pindall's battalion, was transferred to northwestern Louisiana in March to reinforce Confederate forces opposing Banks' campaign.

[31] Parsons' division began moving towards the front lines on April 5, but did not arrive until four days later, too late to participate in the Confederate victory at the Battle of Mansfield.

After their arrival in the afternoon of April 9, Parsons' division formed on the right of the Confederate line as part of the deployments for the Battle of Pleasant Hill.

[31] On March 23, Federal forces commanded by Major General Frederick Steele had left Little Rock with the intention of moving south towards Shreveport to join Banks' campaign.

With insufficient quantities of food and forage, Steele decided to instead move towards Camden on April 12, which the Federal forces occupied three days later.

[34] As Banks' campaign had been defeated, Confederate General E. Kirby Smith decided to take Parsons' and two other divisions into Arkansas to attack Steele, with the march beginning on April 14.

[39] The 9th Missouri Sharpshooter Battalion had 1 man killed and 4 wounded; the unit was cited by Burns for "sturdy and unwavering courage".

[40] When Parsons' men left the camp near El Dorado in August, the division was separated, with Burns' brigade sent to Monticello.