In the end, Walker's most ardent desires would be realized. Lincoln would issue the Emancipation Proclamation in 1863, freeing all slaves in Confederate territory, and two years later the Thirteenth Amendment, banning slavery in the United States, would ratified. While Walker would die just one year before the Nineteenth Amendment gave her the right to vote, she is still, to this day, the only woman to have ever received the Congressional Medal of Honor.

She lit out for the nation's capital and found a city overrun with soldiers wounded during the Second Battle of Bull Run, and an insufficient number of medical professionals struggling to treat them. She went straight to Secretary of War Simon Cameron and presented herself as a willing and able surgeon. Cameron found Walker's reform dress, a shortened dress atop slacks, totally absurd, and would not consider the idea of commissioning a woman for any rank above nurse. He turned her away, but it did not matter.

Walker was determined to be a useful patriot, and her services were readily accepted by Dr. J.N. Green, the lone surgeon of the Indiana Hospital, a makeshift infirmary hastily set up inside the unfinished U.S. Patent Office. Eager for Walker to be compensated, Green requested that Surgeon General Clement A. Finley formally appoint her assistant surgeon, which he refused. Entangled in a long divorce with a philandering husband who impregnated at least two patients, Walker was not a woman of means, yet she returned to work, politely refusing to share Green's salary.

Indiana Hospital soon received additional doctors, but Walker did not hold them in high esteem. By 1861, the Sanitary Commission recommended amputations be conducted when a limb had serious lacerations or compound fractures, but the practice was controversial, with disconcerting mortality rates: Nearly 60 percent of leg amputations done at the knee resulted in death, while less than 20 percent survived hip-level amputations. Walker observed her colleagues senselessly amputating for want of practice. She wrote, "It was the last case that would ever occur if it was in my power to prevent such cruel loss of limbs." She began double-checking their work, surreptitiously counseling soldiers against the surgery when appropriate. Many wrote her thankful letters after the war, reporting their limbs to be fully functional.

Word quickly spread throughout what Walt Whitman called the "mad, wild, hellish" wartime capital: Dr. Mary Walker was a friend to soldiers. Knowing she was bold and skilled, anxious families begged her to seek out their injured sons, brothers and husbands, marooned near raging battles. In an 1862 letter published in The Sibyl, she wrote:

It is literally impossible for one with any force of character and humanity to remain 'in the background,' when convinced by knowledge and reason, that their mission is evidently one that will result in great good in those whose necessities demand that they have not the power to gain for them selves. For such let us labor. Virtue is as much higher than innocence as angers are higher than mortals.

Two years into the Civil War, Walker was mired in a frustrating cycle. She wrote endless letters requesting an official post, and received just as many refusals. Regardless, Walker continued to treat wounded soldiers, and military surgeons and generals on the ground were grateful for her sudden appearances. Dr. Preston King penned a letter describing Walker's contributions in the aftermath of a brutal defeat at Fredericksburg, resulting in 13,000 casualties, but the secretary of war responded that there could never be a commission for her, as there was no "authority of law for making this allowance to you."