He was born at Inverness on 5 June 1828, the younger son of Alexander Fraser (1764?1834) of Dochnalurg and his wife, Marjory (d. 1865), daughter of Captain Alexander Mackintosh. By royal licence on 18 September 1857, in accordance with the will of his maternal uncle, Eneas Mackintosh, he assumed the additional surname of Mackintosh. At the age of fourteen he began his legal apprenticeship in Inverness and in 1849 he was sent to Edinburgh to continue his legal studies at the university where he attended classes in civil and Scots law, conveyancing, and rhetoric. In 1853 he established his own legal practice in Inverness. He retired from legal practice in 1867, and from 1869 to 1873 acted as commissioner on the Mackintosh estates, himself owning small estates outside Inverness. On 12 July 1876 he married Eveline May (d. 1925), only child of Richard David Holland, of Kilvean, Inverness-shire.
Fraser-Mackintosh began his political career in November 1857 when he was elected to the Inverness town council, serving until his resignation in 1862. During the 1860s he was responsible for a series of improvements in the town of Inverness. In February 1874, standing as an independent liberal, he was elected MP for the Inverness burghs seat, defeating the sitting Liberal member, Eneas W. Mackintosh of Raigmore. In his campaign Fraser-Mackintosh was supported by the more radical of the Inverness newspapers, the Advertiser and John Murdoch's Highlander. During the 1870s he was active in a range of causes, especially that of the Gaelic language. After the Education (Scotland) Act of 1872 a campaign to demand a place for Gaelic in the Scottish curriculum was initiated. This was promoted by the Gaelic Society of Inverness, of which Fraser-Mackintosh was one of the founding members in 1871. Minor concessions for the language were secured in the 1870s. Fraser-Mackintosh was also prominent in the successful campaign to endow a chair of Celtic in the University of Edinburgh. During the period from 1874 to 1885 he was popularly known as the Member for the Highlands owing to his popularity among the crofters of the highland counties who were not enfranchised until 1885.
In 1882, along with Donald H. MacFarlane, the member for co. Carlow in Ireland, Fraser-Mackintosh called for the establishment of a royal commission to inquire into the crofting issue. When that commission was appointed (1883) under the chairmanship of Lord Napier, Fraser-Mackintosh was appointed as a member. The Napier commission toured the highlands in 1883 taking evidence and reported the following year. Although few of its recommendations were implemented in later legislation the commission was central in giving greater publicity to the cause of the crofters. In 1885 Fraser-Mackintosh accepted the nomination to stand as a crofter candidate in Inverness-shire, the Scottish county electorate having been greatly expanded by the reforms of 1885. When the Liberal Party divided over the issue of Irish home rule in 1886, Fraser-Mackintosh, alone among the crofter MPs, became a Liberal Unionist. Although a radical on land issues, he was sometimes described as an ?imperialist?. His belief in the repopulation of the highlands stemmed from his awareness of the martial tradition of highlanders and his desire to harness it for the British empire. At the general election of July 1892 he was opposed by a crofter candidate, Dr Charles MacGregor, and defeated.
Fraser-Mackintosh was also a noted historian and genealogist. His primary interest was clan genealogy and the history of Inverness and the surrounding region. His historical columns in the Inverness Advertiser and The Highlander were collected as Antiquarian Notes, published in 1865, reprinted in 1897, and with a second edition in 1913. Invernessiana: Contributions toward a History of the Town and Parish of Inverness, from 1160 to 1599 was published in 1875 and his third major work, Letters of Two Centuries Chiefly Connected with Inverness and the Highlands, from 1616 to 1815, was published in 1890. In addition, Fraser-Mackintosh was a frequent contributor to the Transactions of the Gaelic Society of Inverness. He was awarded the honorary degree of doctor of laws by the University of Aberdeen in 1897 for his contribution to the literature of the highlands. Fraser-Mackintosh died in Bournemouth on 25 January 1901 and was buried in Kensal Green cemetery, London. He was survived by his wife; they had no children.