The following Confederate States Army units and commanders fought in the Second Battle of Winchester. The Union order of battle is listed separately.
Military rank abbreviations
- LTG = Lieutenant General
 - MG = Major General
 - BG = Brigadier General
 - Col = Colonel
 - Ltc = Lieutenant Colonel
 - Maj = Major
 - Cpt = Captain
 
Confederate army
Second Corps, Army of Northern Virginia (22651 officers & men) 
LTG Richard S. Ewell
| Division | Brigade | Regiments and Others | 
|---|---|---|
| 
 Early's Division (6350 officers & men)  | 
Hays' Brigade (1272 officers & men) | 
  | 
| Hoke's Brigade (1750 officers & men)
 
  | 
  | |
| Smith's Brigade (1180 officers & men) | 
  | |
| Gordon's Brigade (1850 officers & men) | 
  | |
| Artillery Battalion (298 officers & men)
 
  | 
  | |
| 
 Johnson's Division (6473 officers & men)  | 
Steuart's Third Brigade (2178 officers & men) | 
  | 
| Nicholl's "Pelican" Brigade (1038 officers & men) | 
  | |
| Stonewall Brigade (1346 officers & men) | 
  | |
| Jones' Second Brigade (1446 officers & men) | 
  | |
| Artillery Battalion (380 officers & men) Ltc R. Snowden Andrews (W); Maj Joseph W. Latimer  | 
  | |
| 
 Rodes's Division (7952 officers & men)  | 
Daniel's Brigade (2157 officers & men) | 
  | 
| Iverson's Brigade (1380 officers & men) | 
  | |
| Doles's Brigade (1329 officers & men) | 
  | |
| Ramseur's Brigade (1023 officers & men) | 
  | |
| O'Neal's Brigade (1685 officers & men) Col Edward A. O'Neal  | 
  | |
| Artillery Battalion (378 officers & men) Ltc Thomas H. Carter  | 
  | |
| 
 Unattached  | 
  | |
| 
 Cavalry  | 
Jenkins's Cavalry Brigade (1185 officers & men) | 
  | 
| 
 Artillery Reserve (85 officers & men)  | 
Crutchfield's Artillery | 
|
| Nelson's Battalion
 
  | 
  | 
References
- Lt. Gen. Ewell's Report in the Official Records, Series I, Volume XXVII/2 [S# 44]
 - Grunder, Charles S. and Beck, Brandon H. The Second Battle of Winchester (2nd Edition). Lynchburg, VA: H.E. Howard, Inc., 1989. ISBN 0-930919-90-4
 - Wittenberg, Eric J. and Mingus Sr., Scott L. The Second Battle of Winchester: The Confederate Victory that Opened the Door to Richmond (1st Edition). El Dorado Hills, CA: Savas Beatie LLC, 2016. ISBN 9781611212891
 - Paths of the Civil War
 
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