In the mid Palaeolithic this area was inhabited by the Neanderthal man, who lived in nomadic groups, and in the Neolithic there was already a town standing, as proven by the Pecho Redondo cave. During the Low Roman Empire it was very populated and it is speculated that the are of Ojén had a nucleus which exploited the agriculture and cattle.

The first time that Ojén is quoted is in the "Chronicle of events of the Cordoba emirs". According to the chronicle, Abderramán III initiated a battle to conquer the rebellion of the Mozarabs (Christians who lived in the Muslim’s lands) and Málaga Muladies. It is known that one of the battles between the rebels and the army took place in front of the walls of the Ojén castle. The revolt of the Mozarabs provoked the existence of the ephemeral kingdom with the capital in Bobastro; in the year 921 Abderramán freed Ojén and its church was converted into a mosque. In 1485 the Muslims surrendered before the king, Fernando el Católico and the town enters the Modern Age. At that time, Ojén sent Marbella to export raisins, dry figs, almonds, silks, wax and honey from its hives, to Africa. The Mudejar Muslims became vassals of Castilla and in 1492 the Catholic Kings took over the kingdom of Granada, ending the reconquest.

Ojén is formed into a counsel and the district’s boundaries are fixed. Ojén depends on Marbella, which nominates a governor with civil and criminal jurisdiction. The Kings would not allow the presence of Muslims at less than a league from the coast and many inhabitants of Marbella establish themselves in Ojén; this measure was taken to avoid the Muslims collaborating with the Turkish and Berber pirates. There were then 114 neighbours in Ojén, four of them were old Christians. In spite of the promise to respect Islamism, the Christians erected a church in 1505, by order of the archbishop of Seville, Diego de Deza. The taxes and the Christianising caused bad feelings between the Moors, until in 1568, during the monarchy of Felipe II, the Moors of Istán produced a rebellion, and in 1569 were joined by the Moors of Ojén, who fled with their families and goods to the nearby sierras abandoning the lands after killing their old Christian neighbours and burning the church, houses and crops. Felipe II nominates the Duke of Medina Sidonia and the Duke of Arcos to pacify the Ronda highland and end the rebellion. In 1570 the war ends and Ojén is repopulated by old Christians. The Moorish problem continues in Spain until in 1609 when the King Felipe III expels the Moors.

In 1772, the British chronicler, Francis Carter, describes Ojén as "a town of affable simple people who don’t know tea and coffee, but enjoy goats milk in their clay mugs". In 1807, Carlos IV gives Ojén its independence from Marbella’s jurisdiction. In 1905, Pedro Fernández sent for the Fuente de los Chorros fountain to be built and in 1906 the Marquis of Larios erected the Juanar Palace as a hunting refuge, where the king Alfonso XIII was once invited. The Juanar Palace was made into a national inn in 1965 and since 1984 is exploited by a workers co-operative from Ojén.