There was initially an Oldowan culture in Socotra. Oldowan stone tools were found in the area around Hadibo by V.A. Zhukov, a member of the Russian Complex Expedition in 2008.

Socotra appears as Dioskouridou ("of Dioscurides") in the Periplus of the Erythraean Sea, a 1st-century AD Greek navigation aid. A recent discovery of texts in several languages, including a wooden tablet in Palmyrene dated to the 3rd century AD, indicate the diverse origins of those who used Socotra as a trading base in antiquity.

In 2001 a group of Belgian speleologists of the Socotra Karst Project made a spectacular discovery. Deep inside a huge cave on the island Socotra they came across a large number of inscriptions, drawings and archaeological objects[10][11] that further investigation showed had been left by sailors who visited the island between the 1st century BC and the 6th century AD. Most of the texts are written in the Indian Brāhmī script, but there are also inscriptions in South-Arabian, Ethiopian, Greek, Palmyrene and Bactrian scripts and languages. This corpus of nearly 250 texts and drawings thus constitutes one of the main sources for the investigation of Indian Ocean trade networks in the first centuries of our era.

A local tradition holds that the inhabitants were converted to Christianity by Thomas the Apostle in AD 52. In the 10th century, the Arab geographer Abu Muhammad al-Hasan al-Hamdani stated that in his time most of the inhabitants were Christians. Socotra is also mentioned in The Travels of Marco Polo; Marco Polo did not pass anywhere near the island but recorded a report that "the inhabitants are baptised Christians and have an 'archbishop'" who, it is further explained, "has nothing to do with the Pope in Rome, but is subject to an archbishop who lives at Baghdad". They were Nestorians but also practiced ancient magic rituals despite the warnings of their archbishop.

In 1507, a Portuguese fleet commanded by Tristão da Cunha with Afonso de Albuquerque landed at the then capital of Suq and captured the port after a stiff battle. Their objective was to set a base in a strategic place on the route to India, and to liberate the presumed friendly Christians from Islamic rule. Tomás Fernandes started to build a fortress at Suq, the Forte de São Miguel de Socotorá. However, the infertility of the land led to famine and sickness in the garrison. Moreover the lack of a proper harbour for wintering led to the loss of many moored Portuguese ships, the most important of which was the Santo António gallion under the command of captain Manuel Pais da Veiga. Thus the Portuguese abandoned the island four years later, as it was not advantageous as a base.

The islands passed under the control of the Mahra sultans in 1511. In 1834, the United Kingdom stationed a garrison on the island. Plans were made to make it a coaling station for ships bound for India, but the climate was considered unsuitable and the British left in 1839. In January 1876, it became a British protectorate along with the remainder of the Mahra State of Qishn and Socotra. The P&O ship Aden sank after being wrecked on a reef near Socotra, in 1897, with the loss of 78 lives.

In October 1967, the Mahra sultanate was abolished. On 30 November 1967, Socotra became part of South Yemen. Since Yemeni unification in 1990 it has been part of the Republic of Yemen.

Somali pirates have begun using Socotra as a refueling stop for hijacked maritime vessels.