During this period, Logan became known as the spokesman for Southern Illinois, also known as Egypt. Believing firmly that a nation divided would not succeed, Logan fought for the North at Bull Run as a civilian. Following the speech, Logan volunteered for military service and rose from colonel to major general. Fighting in eight major campaigns, he distinguished himself at Vicksburg, Mississippi, and commanded the entire Union forces at the Battle of Atlanta. At the war's end he saved Raleigh, North Carolina, from being burned by Union troops enraged over the assassination of President Lincoln.
Many historians consider Logan the premier volunteer general of the Civil War.
After the war, Logan returned to Congress. His concern for veterans led him to take part in Illinois' first veterans memorial service at Woodlawn Cemetery in Carbondale in 1866. In 1868, he became the founder of Memorial Day as a national holiday. In 1871, and again in 1874, Logan was elected to the U.S. Senate. During this campaign, Logan commissioned the painting that became the center panel of Atlanta, Georgia's, famed Cyclorama.