During the Roman era a town named Beit Zacharia was located on the hill, which according to legend was the burial place of the prophet Zechariah.

Although the village had been allotted to the Arab state in the 1947 United Nations proposed partition plan, the area was occupied by Israeli forces during the 1948 Arab–Israeli War and the remaining Arab population was expelled in 1950, after which a new Jewish moshav, now Hebraized as Zekharia, was founded on the site.

The Tell rests upon a high hilltop, whereas the village lay on a slightly elevated part of the valley below, on the northwest side of the hill.

[5][citation needed] According to legend, the body of the prophet Zechariah was found here in 415 CE and a church and monastery were established in the lower village by the same name.

[18] However, by the end of Mamluk era, the village was a dependency of Hebron, and formed part of the waqf supporting the Ibrahimi Mosque.

It had a population of 47 Muslim households (an estimated 259 persons) and paid a fixed tax rate of 33,3% on wheat, barley, olives, beehives, and goats; a total of 11,000 akçe.

[23] A Maqam (shrine) in the village dedicated to the prophet Zechariah was noticed by Edward Robinson in 1838,[24] while van de Velde, recorded its name as Kefr Zakaria in the 1850s.

[26][27] In 1883, the PEF's Survey of Western Palestine described Zakariyya as sitting on a slope above a broad valley surrounded by olive groves.

[35] The village was located inside the territory allotted to a future Arab state in the UN's 1947 partition plan.

[36] In the course of Operation Yoav, the 54th Battalion of the Givati Brigade, found the village "almost empty", as most of the residents had temporarily fled to the nearby hills.

[39] In January 1950 David Ben-Gurion, Moshe Sharett and Yosef Weitz decided to evict the villagers, "but without coercion.

[42] During the 1960s, most of the older buildings in the village were decrepit and unsafe and had to be demolished to make room for new, safer housing.

[46] The site is mentioned in sources as early as the fourth century, in the writings of Sozomenos, and it appears on the Madaba map.

[45] In the 1970s, there was a resurgence of Jewish interest in the site, which became a pilgrimage destination for Jews from Kurdistan, Iraq, Iran, Cochin and elsewhere in India, and elsewhere, who prayed there and lit candles.