Local tradition and Baptist church records indicate that the Zion Hill Missionary Baptist Church was organized in 1852 with the Rev. John Bean as first pastor. The first church building on this site is thought to have been a small log house. On August 15, 1853, Aurin Goodgame Horn donated 3 acres including the graveyard to the Zion Hill Baptist Church.
The oldest marked grave is that of Joseph Wood, who was born in 1792 in North Carolina and died in Jasper County on September 16, 1854.
The original church building was quickly replaced by a board-and-batten structure and in the 1880s, a large frame building. This still until 1967, when it was demolished and replaced by a modern brick edifice outside the cemetery's north fence.
Of over 1,186 graves in Zion Hill Cemetery, 36 are unmarked or unknown. Several were citizens of the Republic of Texas; 75 war veterans are interred on this site. The graves of 102 young children bear witness to the high infant mortality rate among pioneers. Another notable grave is that of the Rev. A. C. Sims (1845-1920), who was born in the Republic of Texas, served in the Confederate Army, and was a pastor of Zion Hill Baptist Church.