The site for the cemetery was bought in 1876/7, and John Houlding's building company was contracted to develop the site with its three mortuary chapels, gatehouses, boundary walls and gates. Houlding, the founder of Liverpool F.C., was also the first Chairman of the Everton Burial Board. Everton Cemetery was officially opened on 16 July 1880. Many of the headstones in Everton Cemetery date back much longer than the opening. Whenever work was undertaken in the city, like widening of roads or dock gates, if this work cut into the city's graveyards, the bodies would be exhumed, and moved to Everton, along with the headstones, and in fact sections of Everton Cemetery contain many of these graves, from the likes of St.Nicholas's, St. George's and St. Anne's to name but a few. On 31 August 1898, Liverpool's Necropolis Cemetery, was closed, due to an edict of the City Council, citing the unsanitary conditions spreading to surrounding neighbourhoods, plus the fact that the cemetery was nearing its full capacity of 80,000 burials. The old headstones were 'dropped' over the graves, and subsequently landscaped in the early 1910s, to make Grant Gardens a public park, which was opened by City Alderman J.R. Grant in 1914. Headstones from 'active' private plots at the Necropolis were removed to Everton Cemetery, along with much older headstones and remains from church graveyards within the city boundaries, when public works, such as road-widening or improvements to the riverside docks were undertaken in the early 1900s, which cut into these old burial sites. The majority of standing Necropolis Headstones at Everton Cemetery are in the centre of Section GEN6; however, there are a few of these headstones placed in other religious denomination sections of the cemetery. Older 'dropped' headstones and remains, from churches within the city, long gone, are buried in the outer boundary sections of Everton Cemetery. The gates to the cemetery, the lodge and the chapel are all Grade II listed buildings.
The head of Australian Aborigine warrior Yagan, after being kept in Liverpool Museum, was buried in the cemetery in 1964, in a box also containing a Peruvianmummy and a Maori's head that had also been kept by the museum. After lobbying of British and Australian governments by Noongar tribal representatives, the head was exhumed in 1997 for repatriation and reburial in Belhus, Western Australia.