Logan showed signs of illness when the 49th United States Congress opened its first official session on December 7, 1886. By mid-December, Logan's arms swelled and his lower limbs were in pain. After several days of intense discomfort, the ailment subsided. He relapsed a few days later and eventually struggled to maintain consciousness. On December 24, Logan's doctor's conceded that the condition may be fatal. Around three o'clock in the afternoon on December 26, Logan died at his home in Columbia Heights, Washington, D.C. After his death, Logan's body lay in state in the United States Capitol. He was buried at United States Soldiers' and Airmen's Home National Cemetery. Logan was the author of two books on the Civil War. In "The Great Conspiracy: Its Origin and History" (1886), he sought to demonstrate that secession and the Civil War were the result of a long-contemplated "conspiracy" to which various Southern politicians had been party since the Nullification Crisis; he also vindicated the pre-war political positions of Stephen A. Douglas and himself. He also wrote "The Volunteer Soldier of America" (1887). His son, John Alexander Logan Jr., was also an army officer and posthumously received the Medal of Honor for actions during the Philippine–American War. His brother-in-law, Cyrus Thomas, participated in the Hayden Geological Survey of 1871.