Roderick Flanagan was the son of Patrick and Martha Flanagan, 'bounty' immigrants from County Roscommon, Ireland. He arrived in Sydney with his family as a young boy in 1840, and in subsequent years attended James Ryder's school, before being apprenticed to a printer. He then found employment at the People's Advocate. In ca. 1849, he briefly moved to Melbourne, where he worked at the Daily News. He returned to Sydney in ca. 1850, and then in 1852, with his brother Edward Flanagan (q.v.), started the short-lived literary magazine, the Weekly Chronicle. With its demise he then worked as a journalist at the Empire and the Sydney Morning Herald.
Whilst at the Empire, and still only in his mid-twenties, Flanagan researched and wrote a series of articles titled 'The Aborigines of Australia', which were published in the Empire at intervals during 1853-1854. Despite their flaws, the articles were remarkable for their often sympathetic view of Aboriginal culture and society, and they were later collected by his brother and published as The Aborigines of Australia (1888). During the 1850s, Flanagan also began working on his history of New South Wales, which he completed by ca. 1860.
Flanagan left Sydney for England in November 1860, to arrange the publication of The History of New South Wales (1862). He died of tuberculosis in London shortly before the work appeared in print.