Clarke's masterpiece, "For the Term of His Natural Life" (1874), is an epic portrayal of the convict system in colonial Tasmania and remains a landmark of Australian fiction. Serialized as "His Natural Life," the novel follows the wrongly convicted Rufus Dawes through brutal suffering at Macquarie Harbour and Port Arthur, exposing the cruelty of colonial punishment. Clarke researched the topic in the Public Library of Victoria and visited the ruins of Port Arthur to lend authenticity to his writing.
His other works include the short story collections "Old Tales of a Young Country" (1871) and "The Mystery of Major Molineux," as well as journalism gathered posthumously in volumes such as "The Future Australian Race." Clarke died in Melbourne in 1881, aged only thirty-five, leaving a lasting legacy in Australian letters.