Upon graduation, Palmer was assigned as a brevet second lieutenant in the Regiment of Mounted Rifles on July 1, 1846. He joined his regiment at Jefferson Barracks, Missouri, on October 29, 1846, and departed with them in December for service in the Mexican War. He was promoted to second lieutenant in the same regiment on July 20, 1847. During the war, he participated in the siege of Vera Cruz, battles of Cerro Gordo, Contreras, Churubusco, Chapultepec, and the capture of Mexico City. He was brevetted first lieutenant in August 1847 for gallant and meritorious conduct in the battles of Contreras and Churubusco. On September 13, 1847, he was brevetted captain for gallant conduct at Chapultepec, where he was severely wounded. He commanded Company B of the police force in Mexico City from December 18, 1847 to June 5, 1848 before returning with his regiment to Jefferson Barracks in July 1848.
Palmer served as the acting regimental adjutant from November 25, 1848 to March 25, 1849, when he was assigned to regimental recruiting service at St Louis. He returned to his regiment at Camp Sumner near Fort Leavenworth in time for its march to Oregon City, arriving there in mid-October. He again served as acting regimental adjutant from October 14, 1849 to May 1, 1850, primarily at Oregon City and Fort Vancouver, then held the actual position until 1854. He and the regiment were back at Jefferson Barracks in 1851. From 1852 to 1854, the regiment participated in Indian campaigns in Texas, assigned at various times to Forts Inge, Ewell and Merrill. He was promoted to first lieutenant January 27, 1853. Palmer was once again on recruiting duty, this time in Baltimore, when he learned that he’d been appointed to the newly organized 2nd Cavalry.
When the 2nd Cavalry was authorized in 1855, Palmer became one of its captains, with a date of rank of March 3, 1855. He joined the regiment at Jefferson Barracks on August 27, 1855 and served in command of Company D. Once the regiment was filled, he marched with the regiment to Texas, arriving at Fort Mason on January 14, 1856. He served there until July, when he and his company were assigned to Camp Verde, about 60 miles northwest of San Antonio. This wasn’t just any frontier post, as it was also home to the camel experiment conducted under Secretary of War Jefferson Davis. Other than an expedition to the headwaters of the Brazos and Colorado rivers in January and February 1858, Palmer remained in command of Camp Verde until May 1858.
He assembled with his company and the rest of the regiment at Fort Belknap in June 1858 for a march to Utah, but the order was revoked. The regiment dispersed to its various forts and camps, but Palmer remained at Fort Belknap until January 1859. He was ordered to Washington and assigned to special duty from January to May 1859 before receiving a leave of absence to visit Europe. He returned to duty in October of 1860, and conducted a detachment of recruits from depots to Texas before rejoining his company at Camp Cooper on January 5, 1861.
Texas seceded very soon after this, and the regiment began its exodus from the state. Palmer started with his company from Camp Cooper on February 21, 1861, and marched to Green Lake. He was joined there by five other companies of the regiment, which formed the first detachment to leave the state. Palmer assumed command of the battalion and moved it to the port of Indianola, a small port 120 miles south of Galveston. They embarked there on a steamship and arrived in New York harbor on April 11, 1861. He proceeded to Washington immediately with his squadron of Companies D and H, where he was employed guarding the Treasury buildings and assisting with the city’s defenses.
Palmer succeeded to a majority in the regiment two weeks later, on April 25, 1861. He commanded the battalion of Regular Cavalry in the campaign of First Manassas, and was brevetted lieutenant colonel for gallant and meritorious services during the Bull Run campaign. Following the battle, he served on a board convened at Washington for examination of officers reported as unable to perform field service in August 1861. He commanded the regiment in the defenses of Washington from August 28 to September 26, 1861. Palmer was appointed a brigadier general of volunteers on September 23, 1861, and continued to serve in the defenses of Washington until March 1862.
During the Peninsula campaign, he commanded a brigade of infantry in Couch’s division of Keyes’ IV Corps, fighting at the siege of Yorktown, Williamsburg, Seven Pines, Glendale and Malvern Hill. Later that autumn, he organized and forwarded regiments of New Jersey and Delaware volunteers, as well as supervising camps of drafted men at Philadelphia.
From December 1862 until the end of the war he was assigned to various duties in the state of North Carolina. These included at various times command of a division of XVIII Corps, the corps itself, the New Bern defenses, the District of Beaufort, and the Department and District of North Carolina. He was promoted to lieutenant colonel of the 2nd Cavalry in December 1863. In March 1865, he participated in the movements of Sherman’s army with his command, and was engaged at Kinston.
In March 1865 he was awarded all the brevet ranks through brigadier general in the Regular Army for “gallant and meritorious service in the field during the war” and major general of volunteers for long and meritorious service. He mustered out of volunteer service on January 15, 1866, and joined his regiment at Fort Ellsworth, Kansas on May 21. He commanded the regiment from May to September, and then took a leave of absence until December. He rejoined the regiment at Fort Laramie, Wyoming, and commanded it from January to August 1867 and again from November 1867 to July 1868.
In 1868, he succeeded to the colonelcy of the 2nd Cavalry, and he spent the remainder of his career on the frontier in what is now Wyoming and Nebraska. He also served on several cavalry boards, including boards for cavalry tactics in 1868, cavalry equipment in 1874, and a new cavalry cartridge in 1875.
Palmer took a leave of absence due to illness from 1876 to 1879, and retired from the Army at his own request on March 20, 1879. Although engaged for a time in civil pursuits in Denver, he spent the majority of the remainder of his life near Washington. Innis Palmer died in Chevy Chase, Maryland on September 9, 1900. He is buried in Arlington National Cemetery.