The Jewish historian Josephus wrote that Ezra died and was buried in Jerusalem. Hundreds of years later, around 1050, a tomb bearing his name was claimed to have been discovered along the Tigris in southern Iraq. The discrepancy troubled no one enough to stop the pilgrimages. Jewish merchants traveling between India and Egypt from the 11th to the 13th century made the tomb a regular stop on their return journeys. Benjamin of Tudela, the great Jewish traveler, visited around 1170 and recorded how both Jews and Muslims honored the site. A fellow traveler told Alharizi that a shepherd had learned the tomb's location in a dream 160 years before his visit. True or not, the story gave the shrine an origin that transcended sectarian boundaries, a discovery revealed by the divine rather than claimed by any single community.

The present buildings are roughly 250 years old. An enclosing wall surrounds a blue-tiled dome sheltering the darih, the windowless mausoleum containing a wooden cenotaph carved with inscriptions. A separate synagogue stands nearby, disused since the mass emigration of Iraqi Jews in 1951-52 but maintained in good repair. T. E. Lawrence passed through in 1916 and called the complex "a domed mosque and courtyard of yellow brick, with some simple but beautiful glazed brick of a dark green colour built into the walls in bands and splashes." He judged it the most elaborate building between Basra and Ctesiphon. Claudius James Rich, documenting the shrine in 1820, noted that a local told him a Jewish man named Koph Yakoob had erected the current building about thirty years prior. Rich described a battlemented wall and a green dome, though later visitors would call it blue. The Tigris itself may have reshaped the site: the 19th-century archaeologist Austen Henry Layard suggested the original tomb had been swept away by the river's shifting course.

During the Mesopotamian Campaign of World War I and the British Mandate that followed, the shrine and its village served as a regular staging post for journeys upriver. British soldiers and administrators mentioned it in military memoirs and travelogues. Sir Alfred Rawlinson, passing through in 1918, observed an unusual detail: the shrine maintained a staff of midwives for the benefit of women who traveled there to give birth. The association of a prophet's tomb with fertility and safe childbirth speaks to how deeply the site was woven into the lives of the surrounding communities, not merely a destination for pilgrims but a functioning part of the social infrastructure of southern Iraq.

The vast majority of Iraq's Jewish population emigrated in 1951-52 during Operation Ezra and Nehemiah, a mass airlift that carried over 100,000 Jews to the newly established state of Israel. The shrine might have been abandoned. Instead, the Marsh Arabs who had long visited the tomb continued their pilgrimages, and Shia Muslims from across southern Iraq adopted it as their own. Hebrew inscriptions on the wooden casket and a dedication plaque remain prominently displayed in the worship room. Large Hebrew letters spelling God's name are still maintained. Until 2003, the small number of Jews remaining in Iraq continued to visit and pray at the site. The tomb endures as a place where the traces of one community's devotion are preserved by another, a quiet monument to the idea that sacred ground belongs to whoever holds it sacred.