After the wound Cooper was furloughed for 60 days in July, but did not return to duty until December 2nd, 1863. He was last reported on a receipt roll for clothing in April of 1864.
The State of Virginia passed multiple Confederate pension laws between 1888 and 1902. Even earlier, a law was passed providing compensation for soldiers who were killed or lost a limb in the war. Cooper applied for pensions in 1878, 1888, and 1902.
Cooper's pension application reads in part:
"I was a soldier in the late war between the States and was at that time a citizen of Russell county & State of Va and still am a citizen of said co & State. I lost my eye at the Battle of Chacellorsville on or about the 3rd day of May 1863. I was at that time in the Confederate service. In crossing breast works my eye was struck I thought with a piece of a shell, which exploded. I was at the same time struck with fragments of the shell on other parts of my body & rendered senseless and was carried away to the hospital. When I sufficiently recovered to examine the character of the injury I found my eye was hurt and Dr Hinkle the attending Physician upon examination of my eye, said it was distroyed, this Physician examined my eye the next day after I received the injury."Cooper's application was approved and he was awarded a one time award of $30. In 1888 he applied for a yearly disability pension and was awarded $30 per year. As the Legislature expanded the scope of the Confederate pensions, Cooper continued to apply and be granted a yearly pension. Upon his death in 1905, his wife applied for and received a pension for his service.
C. W. Powers "...states that he was in the same battle as spoken of by Applicant belonged to same Company & Regt know that applicant was wounded in said battle, his eyes were good & sound that morning before going into the battle, his eye was gone next time I saw him which was when he again returned to the command and entered the service, he was at the same time wounded in the shoulder."
William P. Cooper died on June 17, 1905, just one day past his 72 birthday. In his obituary his old comrade Charles B. Price wrote "He was loyal to the cause of the South, a brave and faithful soldier, an active member of McElhaney Camp, No. 835, U. C. V., a good citizen, and a true man."