This flag was supposed to have been made for the General by his wife, Mary Custis Lee. He began to use it perhaps some time shortly after taking command of the Army of Northern Virginia (June/July 1862). He used it through the Gettysburg campaign (July 1863) and for some time afterward, until the fall of 1863 or winter of 1864 when it was retired and replaced with a new national flag of the pattern adopted by Congress on 1 May 1863.

This flag was used to mark the General's headquarters at any given time. Obviously the unusual star pattern would readily identify the headquarters as those of General Lee. It is said that Mrs. Lee used that pattern to represent the biblical Ark of the Covenant.