MacBain was born 22 July 1855 at Balguish, Glenfeshie (modern-day Badenoch, Inverness-shire) and grew up in poverty.

His parents, John MacBain and Margaret McIntyre were not recorded as married when his birth was registered 9 August 1855.

[1] A native Gaelic speaker, he learned English at Insh General Assembly school, five miles from Kingussie, in Badenoch (1863–1870), whose teacher was Alexander Mackenzie.

During the last two decades of his life, MacBain was one of the leading figures in a Gaelic intellectual circle which met in Inverness and Edinburgh.

[2] MacBain published a critical edition of the Book of Deer and contributed entries on the Picts in Chambers's Encyclopaedia, articles for magazines and newspapers and reviews for the Transactions of the Gaelic Society of Inverness (1880–1903).