According to a legend, Beit Hanoun was the capital of the Philistine King Hanoun, who fought the Assyrians in the 8th century BCE.
The Ayyubids defeated the Crusaders at a battle in Umm al-Nasser hill, just west of Beit Hanoun in 1239, and built the Umm al-Naser Mosque ("Mother of Victories Mosque") there in commemoration of the victory. A Mamluk post office was located in Beit Hanoun as well.
Incorporated into the Ottoman Empire in 1517 with all of Palestine, Beit Hanoun appeared in the 1596 tax registers as being in the Nahiya of Gaza, part of Gaza Sanjak. It had a population of 36 Muslim households and paid a fixed tax rate of 33,3% on wheat, barley, summer crops, fruit trees, occasional revenues, goats and/ or beehives; a total of 9,300 akçe.
Pierre Jacotin named the village Deir Naroun on his map from 1799.
In 1838 Edward Robinson passed by, and described how "all were busy with the wheat harvest; the reapers were in the fields; donkeys and camels were moving homewards with their high loads of sheaves; while on the threshing-floors near the village I counted not less than thirty gangs of cattle.." He further noted it as a Muslim village, located in the Gaza district.
In May 1863, the French explorer Victor Guérin visited the village. Among the gardens he observed indications of ancient constructions in the shape of cut stones, fragments of columns, and bases. Socin found from an official Ottoman village list from about 1870 that Beit Hanoun had 94 houses and a population of 294, though the population count included men, only. Hartmann found that Bet Hanun had 95 houses.
In 1883 the Palestine Exploration Fund's Survey of Western Palestine described it as a small adobe village, "surrounded by gardens, with a well to the west. The ground is flat, and to the east is a pond beside the road."
British Mandate era
In the 1922 census of Palestine conducted by the British Mandate authorities, Beit Hanoun had a population of 885 inhabitants, all Muslim, decreasing in the 1931 census to 849, still all Muslims, in 194 houses.
Beit Hanoun 1931 1:20,000
Beit Hanoun 1945 1:250,000
In the 1945 statistics Beit Hanun had a population of 1,680 Muslims and 50 Jews, with 20,025 dunams of land, according to an official land and population survey. Of this, 2,768 dunams were for citrus and bananas, 697 were plantations and irrigable land, 13,186 used for cereals, while 59 dunams were built-up land.
In the 1948 Arab–Israeli War, the vicinity of Beit Hanoun, and later Beit Hanoun itself, served as an Israeli tactical wedge (Beit Hanoun wedge) to halt the movement of the Egyptian army from Ashkelon to forces to the south in the area that later became the Gaza Strip.
While under control of Egyptian authorities, Egypt complained to the Mixed Armistice Commission that on the 7 and 14 October 1950 Israeli military Forces had shelled and machine-gunned the Arab villages of Abasan al-Kabera and Beit Hanoun in Egyptian controlled territory of the Gaza strip. According to Egypt this action caused the death of seven and the wounding of twenty civilians.
The body a person killed in the home of 'Abd al-Hafez Hamad. Six members of one family were killed when their house was bombed on the night of 8 July 2014.
According to the Palestinian Authority, 140 Palestinians were killed by Israeli forces in Beit Hanoun from September 2000 to November 2006.
The Israeli army besieged Beit Hanoun from 15 May to 30 June 2003, during which it demolished dozens of houses, razed large areas of agricultural land and largely destroyed the civilian infrastructure of the town. During the Raid on Beit Hanoun in 2004, the town was besieged for 37 days. About 20 Palestinians were killed and again immense damage was caused to property and infrastructure. The infrastructure of Beit Hanoun was heavily damaged during an incursion by Israeli forces in 2005.
Following the removal of Israeli settlers from Gaza in August 2005 the 2006 shelling of Beit Hanoun, killed 19 Palestinian civilians. In December 2006, the UN appointed a fact-finding commission led by Anglican Archbishop Desmond Tutu to investigate the attack. However, Tutu and the other members were not granted permission to travel by Israel and the investigation was cancelled. Tutu's final report to the United Nations human rights council concluded, however, that "[I]n the absence of a well-founded explanation from the Israeli military – who is in sole possession of the relevant facts – the mission must conclude that there is a possibility that the shelling of Beit Hanoun constituted a war crime."
On 27 March 2007, sewage water flooded the northern Umm al-Nasser suburb of Beit Hanoun, killing five people.
Beit Hanoun was hit several times by shells and rockets during the 2014 Israel–Gaza conflict. The shelling of an UNWRA Elementary school by Israel killed 11-15 people, including women and children. The Israeli Defense forces claimed that "the IDF encountered heavy fire in vicinity of the school, including anti-tank missile... [and] that an errant mortar did indeed land in the empty courtyard of the school."