Noyes was then sick in a hospital at Frederick, Maryland in July 1863 before returning to the Army on the Rappahannock.

Noyes was promoted to brevet captain on August 1, 1863, for "Gallant and Meritorious Services" at the Battle of Brandy Station, Virginia.

Noyes was brevetted major retroactive to April 2, 1865, for "Gallant and Meritorious Services" at the Capture of Selma, Alabama.

He returned to frontier duty and was assigned to Fort Laramie from October 1875 until early 1876, when he was ordered to move his Company I of the 2nd Cavalry to Fort Fetterman, Wyoming Territory, in order to participate in the Big Horn Expedition of March 1–27, 1876.

During this campaign, Noyes was given command of the 3rd Battalion, consisting of Companies I and K of the 2nd U.S. Cavalry at the Battle of Powder River in Montana Territory.

Upon returning to Fort Laramie, Noyes would be court-martialed for his actions during the battle in unsaddling his company and therefore rendering it unable to support the remainder of the command fighting in the village.

He was found guilty on May 2 but allowed to rejoin his regiment and command a five-company battalion of the 2nd Cavalry during the Big Horn and Yellowstone Expedition from May 23 to October 28, 1876, being engaged in the Battle of Prairie Dog Creek on June 9 and the Battle of Rosebud on June 17, 1876.

Noyes served on Mounted Recruiting Service from October 1878 to September 30, 1879, and was promoted major, 4th Cavalry effective June 14, 1879.

He died at his home in Berkeley on July 13, 1919,[3][4] at the age of 79 and is buried in San Francisco National Cemetery.