Idhna's site was inhabited since Canaanite times, evident from ancient remains found in the town. The town is identified with the biblical city of Dannah, mentioned in Joshua 15:49. Hebrews, Byzantines and Arabs succeeded in gaining control of the town and coins, statues, tombs and pottery dating from these various rulers were found in the town.
Ottoman era
Idhna was incorporated into the Ottoman Empire in 1517 with all of Palestine, and in 1596 it appeared in the tax registers as being in the nahiya of Halil in the liwa of Quds. It had a population of 68 households, all Muslim. They paid a fixed tax rate of 33,3% on agricultural products, including wheat, barley, olives, vineyards, fruit trees, goats and/or beehives; a total of 19,000 akçe. All of the revenue went to a waqf. Edward Robinson, who visited Idhna in 1838, recorded that the town's two parts were led by a sheikh and the inhabitants of each part followed and backed their respective sheikh in internal quarrels. Adjacent to Idhna are the ruins of the original village which is totally covered by cultivable fields. Marbletesserae were found on the site. Idhna was further noted as a Muslim village located between the mountains and the plain of Gaza, but subject to the government of el-Khuhlil. Victor Guérin visited Idna in June 1863 and described a village with almost 500 inhabitants, divided into two districts, each ruled by a sheikh. Many houses, especially a small Bordj, had substructures of stone, which, to all appearances, were dating back to antiquity. An Ottoman village list of about 1870 showed that Idna had 22 houses and a population of 108, though the population count included only men. In 1883 the PEF's Survey of Western Palestine described Idhna as "a small village on the south slope of a hill divided by a small depression into two." SWP further found that near the town were several large caves with niches for lamps or skulls.
In the 1922 census of Palestine, conducted by the British Mandate authorities, Idna had a population of 1,300, all Muslim, increasing in the 1931 census to 1,719, still all Muslim, in 317 houses. In the 1945 statistics the population of Idna was 2,190, all Muslims, who owned 34,002 dunams of land according to an official land and population survey. 528 dunams were plantations and irrigable land, 14,481 for cereals, while 153 dunams were built-up land.
Since the Six-Day War in 1967, Idhna has been under Israeli occupation. The population in the 1967 census conducted by the Israeli authorities was 3,713. On 25 April 2015 Mahmoud Abu Jheisha, 20 years old, from Idhna was shot dead in Hebron after he had been accused of stabbing an Israeli soldier.
