In 1517, the village was included in the Ottoman empire with the rest of Palestine, and in the 1596 tax-records it appeared as Farha, located in the Nahiya of Jabal Quba, part of Nablus Sanjak. The population was 17 households, all Muslim. They paid a fixed tax rate of 33,3% on agricultural products, such as wheat, barley, summer crops, olive trees, goats and beehives, in addition to occasional revenues and a fixed tax for people of Nablus area; a total of 2,800 akçe. Pottery sherds from the early Ottoman era has also been found here. In 1838, Furkha was noted as village in the Jurat Merda area, south of Nablus. In 1870, Victor Guérin on his travels noted Farkha as a "considerable" village, located on a mountain peak. In 1882, the PEF's Survey of Western Palestine described Furkhah as: "An ancient village in a very strong position on a steep hill-top. The houses are of stone, and there are three sacred tombs, including Haram en Neby Shit, on the south. The fountain of Ain Yambua, in the valley, gives a supply of fine water, and there are two other springs east of the village. The place is evidently an ancient site. The hills around it are very steep and rocky."
In the 1922 census of Palestine conducted by the British Mandate authorities, Farkha had a population of 210 Muslims, increasing in the 1931 census to 304 Muslims in 54 occupied houses. Tawfiq Canaan mention the custom of Mafazeh at the top of the ascent of Farkah; “a traveller after climbing a high mountain raises a heap of stones, or throw a stone on an existing heap, saying at the same time prayer as a mark of thanks to God that he has overcome a difficulty." In the 1945 statistics the population was 380 Muslims while the total land area was 5,675 dunams, according to an official land and population survey. Of this, 1,753 were allocated for plantations and irrigable land, 1,301 for cereals, while 14 dunams were classified as built-up areas.
Since the Six-Day War in 1967, Farkha has been under Israeli occupation. After the 1995 accords, Israel and Israeli settlements got 80% of the water from the Western Aquifer, leading often to severe shortages of water in Farkha. After 1995, 48% of village land is defined as Area A land, 21.6% is Area B, while the remaining 30.4% is defined as Area C land. As of 2013, the plans for the Segregation Wall would isolate the village from much of its land behind the wall.