The Gaelic name Sgalpaigh na Hearadh - 'Scalpay of Harris,' to distinguish it from the other Scalpay off Skye - is borrowed from Norse. The toponymist Mac an Tàilleir argued in 2003 that it comes from a Norse word meaning 'ship island.' The geographer Hamish Haswell-Smith preferred Skalprøy, 'scallop island.' Both are plausible. Either way, the name reaches back to the centuries when Norse-speaking sailors held these waters and gave their names to the islands they passed. The largest of Scalpay's many lochans is Loch an Duin, the 'Loch of the Fort,' which contains a small island still bearing the remains of an Iron Age dun. Eilean Glas, the tied islet on the east coast, was the site in 1789 of the first lighthouse built anywhere in the Hebrides.

In April 1746, the Jacobite cause died at Culloden Moor. The defeated Prince Charles Edward Stuart - 'Bonnie Prince Charlie' - became the most hunted man in Britain, with £30,000 on his head, and for the next five months he ran across the Hebrides one step ahead of redcoats and rumour. He came to Scalpay in late April, taking shelter for a few nights with the tenant farmer Donald Campbell, who refused to betray him despite the bounty. From Scalpay the prince made his way to Stornoway, then back south through the Uists, finally escaping to France in September. The Scalpay episode lasted barely a week. It is the kind of week that locals were still telling stories about two centuries later.

Scalpay's fortunes through the 20th century rose and fell with fish. In 2001 the island had 322 people, most working in fish farming and prawn fishing. A salmon factory provided steady employment from 2001 until it closed in 2005. The last general shop on the island closed in 2007. By 2011 the population had fallen 9 percent to 291, while Scottish island populations as a whole were growing. Then, in 2011, Scalpay's owner Fred Taylor announced he intended to hand the entire island over to the people who lived there. The islanders voted to accept the gift, formed a partnership with the community-owned North Harris Trust, and in 2013 became, formally, their own landlords. In 2012 they opened Buth Scalpaigh, a community shop and café. The bridge from Harris remains the lifeline. The island is now, for the first time in centuries, its own.