The village was situated in a relatively flat area on the central coastal plain. It was linked to Lydda and Jaffa by the highway that ran between these two cities. In the late nineteenth century, Fajja was a small village built of adobe bricks. It was about 1 km east of the Zionist settlement of Petach Tiqwa, which had been founded in 1878. During the Mandate period some newer houses were constructed of concrete. During that time, the entire population of Fajja was Muslim. The village had an elementary school, opened in 1922, whose enrollment reached 781 by the mid-1940s (including 10 female students). The residents cultivated crops, such as grain and vegetables, on the greater part of their land. In 1944/45 a total of 602 dunums was devoted to citrus and bananas and 2,457 dunums were allotted to cereals; 53 dunums were irrigated or used for orchards. Water for agriculture was obtained from rainfall and wells. Faija was constructed over the remains of an archaeological site that contained fragments of columns (shafts and capitals), the foundations of buildings, and a cistern.
Attacks on Fajja began as early as 20 May 1947, when a Palmach unit infiltrated the village on the pretext of apprehending thieves who had murdered two people in Petach Tiqwa. According to the History of the Haganah, shooting broke out when the unit approached the coffeehouse where the thieves were allegedly hiding and two villagers were killed; 'explosives experts stormed the coffee-house under heavy covering fire, planted an explosive charge and ignited it.' The 'Book of the Palmach' reports that the explosion was unnecessarily delayed and although the coffeehouse was destroyed, no one was harmed.
The next recorded attack was launched by the Irgun on 17 February 1948, after which some villagers fled, according to Israeli sources. Israeli historian Benny Morris also states that Fajja was hit 'repeatedly' by both the Haganah and Irgun in the early months of the war; by May, only several dozen residents remained. Haganah intelligence officers met on 9 May and decided that this 'bothersome element' should be expelled. The last villagers left on 15 May, according to Israeli military intelligence, because of 'pressure by us—a whispering operation.'
By June, the Jewish National Fund (JNF) had set in motion the process of destroying Fajja, among other villages. On 14 June, Ezra Danin, a senior Haganah intelligence officer and official of the Jewish Agency, reported to JNF official Yosef Weitz on the progress made in destroying Fajja. Two days later, Israeli prime minister David Ben-Gurion wrote in his diary that Fajja and two other villages had been destroyed.
The site was initially occupied in the early 1950s by a transit camp for new immigrants called 'Ammishav (140164), but now it has become an eastern suburb of the settlement of Petach Tiqwa (139166), which had been established west of the village in 1878.
The village has been completely razed except for one house and a pond. Eucalyptus trees and cactuses further mark the site. The surrounding land is partly occupied by buildings; the rest is cultivated.