The largest of the 350 islands in the Canarreos Archipelago (Archipiélago de los Canarreos), the island has an estimated population of 100,000. The capital and largest city is Nueva Gerona in the north, and the second largest and oldest city is Santa Fe in the interior. Other communities include Columbia, La Demajagua (formerly Santa Bárbara), Mac Kinley, Cuchilla Alta, Punta del Este, Sierra de Caballos and Sierra de Casas.

Little is known of the pre-Columbian history of the island, though a cave complex near the Punta del Este beach preserves 235 ancient drawings made by the native population. The island first became known to Europeans in 1494 during Christopher Columbus's second voyage to the New World. Columbus named the island La Evangelista and claimed it for Spain. The island was also known as Isla de Cotorras (Isle of Parrots) and Isla de Tesoros (Treasure Island) at various points in its history. Pirate activity in and around the area left its trace in English literature. Both Treasure Island by Robert Louis Stevenson and Peter Panby J. M. Barrie draw on accounts of the island and its native and pirate inhabitants, as well as the long dugout canoes that both pirates and the indigenous peoples used and the American crocodile (Crocodylus acutus).

Following its defeat in the Spanish–American War and the Cuban War of Independence, Spain dropped all claims to Cuba under the terms of the 1898 Treaty of Paris. The Platt Amendment of 1901, which defined Cuba's boundaries for the purposes of U.S. authorities, left the U.S. position on sovereignty over Isla de la Juventud undetermined. This led to competing claims to the island by the United States and Cuba. In 1907, the U.S. Supreme Court decided, in Pearcy v. Stranahan, that control of the island was a political decision, not a judicial one. In 1916, a pamphlet titled Isle of Pines: American or What? called for the U.S. to annex or purchase the island to settle the issue.

In 1904, Cuba and the United States negotiated and signed the Hay-Quesada Treaty, which recognized Cuba's sovereignty over the island. The U.S. Senate ratified this agreement on March 13, 1925, over the objections of some four hundred United States citizens and companies, who owned or controlled about 95% of the island's land.

Prior to 1976, the island was part of La Habana Province. With the political and administrative reorganization of Cuban provinces in 1976, the island was given the status of "special municipality" Fidel Castro presided at a ceremony changing the name of the island from Isla de Pinos to Isla de la Juventud on 3 August 1978. This was the realization of a promise that he had made in 1967, when he said "Let’s call it the Isle of Youth when the youth have done something grand with their work here, when they have revolutionized the natural environment, when they see the fruits of their labor and have revolutionized society here.The island has a mild climate, but is known for frequent hurricanes. It is a popular tourist destination, with many beaches and resorts, including Bibijagua Beach. The main transportation to the island is by boat or aircraft. Hydrofoils (kometas) and motorized catamarans will make the journey from Batabanó to Nueva Gerona in between two and three hours. A much slower and larger cargo ferry takes around six hours to make the crossing, but is cheaper.

In 1926, Cuba erected a model penitentiary of panopticon design on the outskirts of Nueva Gerona, Presidio Modelo, 1926 and 1928 Cuban leader Fidel Castro, after leading the failed attack on the Moncada Barracks in July 1953, was imprisoned in it from 1953 to 1955 by the regime of Fulgencio Batista, as was his brother Raúl.] Following the Cuban Revolution, the same facility was used to imprison the new regime's enemies and political dissidents. They included Huber Matos, an officer in the revolutionary army who attempted to resign and who said he was tortured there and Armando Valladares, who wrote a memoir describing the prison's harsh conditions and cruel treatment of prisoners of conscience and political prisoners. Presidio Modelo ceased functioning as a prison in 1967. It has been declared a national monument and its hospital rooms converted into a museum. Its functions are now carried out in more modern facilities, including one minimum security prison (Prison El Guayabo) and four correctional facilities: Center for Reeducation of Minors, Correctional Los Colonos, Paquito Rosales Cueto (1 y 11), and Prison la 60 (Columbia).