When the Civil War broke out, Ector enlisted as a private in the 3rd Texas Cavalry Regiment of the Confederate army.

At the Battle of Stones River on December 31, 1862, Ector commanded a brigade in John P. McCown's division, William J. Hardee corps.

[1] At the Battle of Chickamauga on September 19–20, 1863, Ector's brigade was part of States Rights Gist's division, William H. T. Walker's corps.

[2] During the Atlanta Campaign in the summer of 1864, Ector's brigade was in Samuel G. French's division, Leonidas Polk's corps.

The war ended before his recovery was complete, although he did travel to Mobile, Alabama, to assume command of the defenses there late in early 1865.

Three brigades under Randall L. Gibson, James T. Holtzclaw, and Ector fought in the Battle of Spanish Fort on 8 April 1865 near Mobile.

The much larger Union army seized part of the defenses, forcing the Confederates to evacuate Spanish Fort with the loss of 93 killed, 395 wounded, 250 missing, and 50 cannons.