In 1517, the village was incorporated into the Ottoman Empire with the rest of Palestine, and in 1596, Kafr Harit appeared in Ottoman tax registers as being in nahiya (subdistrict) of Jabal Qubal, part of the Sanjak of Nablus. It had a population of 54 households, all Muslim. They paid taxes on occasional revenues, goats and/or beehives, and a fixed amount; a total of 22,500 akçe. Sherds from the early Ottoman era have also been found here.
In 1838, Edward Robinson noted it as a village, Kefr Harith, in the Jurat Merda district, south of Nablus.
In 1870 Victor Guérin reached the village, after walking through "beautiful plantations of figs and olives". He estimated it had 600 inhabitants. The name of this place was given to Guérin as Kefil Haris. The Wely marked on the Palestine Exploration Fund 1880s map as Sheikh Ata, 1 mile north-east of Kefr Haris, is called by him Sheikh Khather. He also calls attention to the remains of an old watchtower built of large, well-cut stones, between Deir Estia and Kefr Haris. At the latter place he found two broken marblecolumns built up in the wall of the mosque.
In 1882, PEF's Survey of Western Palestine described Kifl Haris as a "somewhat small village on high ground, with olive groves to the east. It has three sacred places, Neby Kifl, Neby Nun, and Neby Lusha."
In the 1945 statistics the population was 770 Muslims while the total land area was 9,393 dunams, according to an official land and population survey. Of this, 4,117 were allocated for plantations and irrigable land, 2,131 for cereals, while 32 dunams were classified as built-up areas.
According to a Samaritan tradition, noted in 1877, the tombs of Joshua and Caleb were in Kifl Haris.
Biblical tradition places the tomb of Joshua, Caleb, and Nun according to Joshua 24:30 in Timnath-heres which is attributed to be the current location of Kifl Haris. Thousands make the pilgrimage to the tombs on the annual commemoration of Joshua's death, 26th of Nisan on the Hebrew calendar.
42% of the village land is classified as Area B land, while the remainder 58% is Area C. Israel has confiscated 361 dunams of land from Kifl Haris in order to establish the Israeli settlement of Ariel.
On 14 March 2013,Adele Biton was critically injured (later dying from her injuries), and her mother and two sisters were moderately injured, after their car crashed after Palestinians threw stones their way near the village. Five youths from Kifl Haris were charged by a military court for responsibility for the incident, and as of February 2015 the case has not yet been concluded.
In June 2014, Jamil Ali Abed Jabir died during a night raid by the Israeli army. Locals say he suffered a heart attack while defending his home. According to an Israeli army spokesman, his house wasn't raided.
In 2015, an Israeli tour of the site was preceded by a convoy of military vehicles which closed off the town entrances and imposed a shutdown of all the village shops so Israeli tourists could visit the tomb for several hours.