Edmund Burke Whitman was born in East Bridgewater, Massachusetts, on October 18, 1812, the son of farmer Alfred Whitman, and his wife, Betsey Robbins. He left home at 15 and worked in an apothecary shop in Vermont; after taking several other short-term jobs in teaching and sales, he enrolled as a charity student at Phillips Exeter Academy and subsequently Harvard College. He received his A.B. degree from the latter in 1838, followed by his A.M. in 1841, and thereafter became headmaster of the Hopkins Classical School in Cambridge, Massachusetts. He was involved in antislavery and temperance societies, and in 1855 moved to Lawrence, Kansas, to join the struggle to make that territory a free state; while there, he befriended abolitionist John Brown.
In October 1862, Abraham Lincoln appointed Whitman captain and assistant quartermaster, assigned to duty in Covington, Kentucky, with Brigadier General Green Clay Smith's brigade. In 1865, he was promoted to chief quartermaster, District of Tennessee, and was stationed at Murfreesboro. After the war Whitman became assistant quartermaster in charge of national cemeteries and mortuary records for the same district. Charged with inspecting cemeteries and battlefields, he located thousands of Union soldiers buried in Tennessee, Kentucky, Georgia, and Alabama, and oversaw the relocation of over 100,000 Union bodies. He left the service in 1868, taught briefly in Louisville, Kentucky, and returned to Cambridge, where he lived until his death on September 2, 1883.
On August 30, 1839, he married Nancy Russell in Kingston, Massachusetts, and they had four children: Amelia (b. 1840), Alfred (b. 1841), Russell (b. 1844), and James (b. 1847). After her early death, he married Lucretia Clapp on October 25, 1858, and they had a son named Edmund, born around 1860.