The Cooktown cemetery has been in continuous use since the town was established in October 1873. The cemetery was proclaimed in 1875 with trustees representing each of the denominations in Cooktown; Church of England, Roman Catholic, Presbyterian, Hebrew and Wesleyan Methodist. Despite the large Chinese population there, no Chinese representative was appointed.
The entrance gate faces the road to the Palmer River, where gold discoveries led to Cooktown becoming a port. An internal road leads from the gate and forks in the middle of the reserve. The track to the west terminates at a Chinese Shrine with a low concrete altar. Nestled amongst the trees in the north-west of the cemetery is a brick well, evidence of the Chinese market gardeners who once worked there.
The rest of the site is divided into denominations by the unsealed paths. Significant graves within the site include that of Mary Watson who died of thirst escaping Lizard Island, 90 kilometres to the north-east; mariner Albert Ross Hovell, son of the explorer William Hovell, known for his involvement in 'blackbirding', or procuring Islanders to work as labourers; and Mother Mary De Sales Meagher, founder of the Sisters of Mercy Convent in Cooktown.