In 1880, he volunteered and was selected for the Howgate expedition, which was canceled. However, the next year he was detailed as first sergeant for the ill-fated Lady Franklin Bay Expedition under Adolphus Greely. Over the three years of this expedition he continuously kept a journal. Among the men to die on this expedition was James Booth Lockwood, second-in-command of the expedition and Brainard's companion on many excursions, including their record breaking push north to 83°23 '30". Brainard wrote: Shortly before rescue, in the spring of 1884, freezing, starving, and suffering from scurvy, he wrote: "Our own condition is so wretched, so palpably miserable, that death would be welcomed rather than feared ..." Brainard was one of only six survivors rescued by Rear Admiral Winfield Scott Schley on June 22. On that day, he was reportedly too weak to hold his pencil to make a note in his log. He was awarded the Back Grant by the Royal Geographical Society in 1885.
Later military career
Brainard was commissioned second lieutenant in the 2nd Cavalry in 1886 "as recognition of the gallant and meritorious services rendered by him in the Arctic expedition of 1881–1884." He then had the distinction of being the only living officer in the US Army commissioned for specific services. He served as chief commissary of the military forces in the Philippines during the Spanish–American War in 1898. Brainard was a charter member of, and actively involved in, The Explorers Club, serving as its fourth president from 1912 to 1913. After receiving a World War I promotion to brigadier general in 1917, he served as military attaché of the US embassy in Portugal from 1918 until his retirement in 1919. As military attaché in Portugal he was made Knight of the Order of Aviz on March 30, 1918.
Post-retirement
Brainard was awarded the Charles P. Daly Medal by the American Geographical Society for his arctic exploration in 1926, and in 1929 was awarded The Explorers Club Medal. On January 27, 1933, Brainard was awarded the Purple Heart for his wounding in the Battle of Little Muddy Creek on May 7, 1877, one of only two medals ever awarded for events of the AmericanIndian Wars. He was elected an honorary member of the American Polar Society in 1936, on his 80th birthday. Brainard married twice, first to Anna Chase in 1888, then to Sara Hall Guthrie in 1917, leaving no children and one stepdaughter, Elinor, from his second marriage. Brainard died, aged 89, on March 22, 1946, and was buried in Arlington National Cemetery, joined by his second wife in 1953. He was the last survivor of the Greely Arctic Expedition.