A 1692 depiction of Canaan, by Philip Lea.
Tel Esur was known locally as a Tell el-Asawir. It appears in a map drawn by French geographer Pierre Jacotin from 1799. American archaeologist and biblical scholar William F. Albright visited the site during his 1923 trip to Mandatory Palestine. He recalled the opinion of German scholar Albrecht Alt that Tel Esur is the site of an ancient city called "Yaham", mentioned in the sources of the 15th century BCE Egyptian pharaoh Thutmose III, who campaigned against a coalition of Canaanite city-states, led by the king of Megiddo, located just north of the Menashe Heights. According to the Egyptian account, Thutmose III camped in Yaham before he marched on Megiddo to fight the Battle of Megiddo. Albright stated that the location of the site corresponds with the geographic descriptions of the Egyptian sources, and his discovery of Bronze Age pottery while surveying the mound further confirmed this identification in his opinion. Today however, Yaham is identified with a site located in Kafr Yama in Zemer, some 10 kilometers south of Tel Esur.
The discovery of the larger site around Tel Esur and its springs occurred in 1977, when during the digging of a water reservoir south of the mound. A salvage excavation was conducted by archaeologists Azriel Zigelman and Ram Gofna of the Tel Aviv University. They discovered two settlement layers, one from the Chalcolithic period (the last period of the Stone Age) and the Early Bronze Age. The former included the foundations of structures made of rough stones and some installations. These are dated to the early Chalcolithic (c. 6000 years ago). The latter included the foundations of massive structures made of large stones. The widest wall measured 1.7 meters wide. The pottery there is dated to the Early Bronze Age I period (3300–3000 BCE).
A survey and an excavation was conducted in 1993 by Eli Yanai of the Israel Antiquities Authority. It revealed the massive extent of the site during the Early Bronze Age, as well as settlement remains from the Neolithic and Chalcolithic periods, and sherds from the Byzantine and Ottoman periods.
En Esur was excavated by professional and volunteer archaeologists over two and a half years beginning in January 2017, with the research overseen by archaeologists Itai Elad and Yitzhak Paz. The work was organized in part by the Israel Antiquities Authority and financed by Netivei Israel, Israel's national transportation infrastructure company. During the process of excavation, archaeologists found a temple within the city that was built approximately 2,000 years before the rest of the site.
In an announcement of their discovery, researchers called En Esur "cosmopolitan" and the "New York City of the early Bronze Age".