It was named for the Prophet Zechariah who was killed in the Temple. (2 Chronicles 24:20-21). The Talmud Yerushalmi relates that this not only happened in the Temple, but it was Yom Kippur that coincided with Shabbat. The Talmud Bavli relates that his blood was unable to be cleaned from the Temple floor, and when the Babylonians came it began to boil. It was not appeased until many Jews lost their lives. It is not know for how long the site has been associated with the grave of Zechariah ben Yehoiada, but the earliest known source are the writings of Menachem HaChevroni in 1215.
Despite this the site has played a major role in the history of the Jewish people of Jerusalem. The site became associated with the destruction of the First Temple, Jews would go to mourn on the 9th of Av and read the the book of Lamentations there. This site was also a focal point for prayers for assistance. There are two documented stories that told of Jews congregating at the “tomb” to pray for rain during drought years (in the years 1651 and 1690) which succeeded in stopping the drought.
Designs in the structure would seem to indicate that the monument was constructed some time during the Hellenistic period. The structure is actually not a tomb but a monument called a “Nefesh” (Tomb stone) next to a tomb. It is thought to be associated with tombs of the Benei Hezir (2nd Chronicles 26:21) located adjacent to the monument.