In November 1842, McClernand married Sarah Dunlap of Jacksonville, Illinois, a close friend of Mary Todd Lincoln. Sarah was a daughter of James Dunlap, who served as a quartermaster in the Union Army during the Civil War, eventually appointed to the rank of brevet major general. John and Sarah's son, Edward John McClernand, was notable as a U.S. Army brigadier general in the Indian Wars and later in the Philippines. After Sarah's death, McClernand married her sister, Minerva Dunlap.