The book tells the adventures of five Americans on an uncharted island in the South Pacific. The story begins in the American Civil War, during the siege of Richmond, Virginia, the capital of the Confederate States of America. As famine and death ravage the city, five northern prisoners of war decide to escape by the unusual means of hijacking a balloon. The five are Cyrus Smith, a railroad engineer in the Union army (named Cyrus Harding in some English translations); his black manservant Neb (short for Nebuchadnezzar), whom Verne repeatedly states is not a slave but an ex-slave who had been freed by Smith; the sailor Bonadventure Pencroff (who is addressed only by his surname, but his "Christian name", Bonadventure, is given to their boat; in other translations, he is also known as Pencroft); his protégé Harbert Brown (called Herbert in some translations), a young boy whom Pencroff raises as his own after the death of his father (Pencroff's former captain); and the journalist Gedéon Spilett (Gideon Spilett in English versions). The company is completed by Cyrus' dog 'Top'.
After flying in stormy weather for several days, the group crash-lands on a cliff-bound, volcanic, unknown (and fictitious) island, described as being located at 34°57′S 150°30′W, about 2,500 kilometres (1,600 mi) east of New Zealand. (In reality, the closest island is located at 27.6°S 144.36°W. In location and description though, the phantom island Ernest Legouve Reef may correspond to the rock that is left of the mysterious island at the end of the novel. ) They name it "Lincoln Island" in honor of American President Abraham Lincoln. With the knowledge of the brilliant engineer Smith, the five are able to sustain themselves on the island, producing fire, pottery, bricks, nitroglycerin, iron, a simple electric telegraph, a home on a stony cliffside called "Granite House", and even a seaworthy ship. They also manage to figure out their geographical location.