When archaeologists excavated the Thainstone Business Park in 2018, they uncovered a Middle Bronze Age roundhouse from between 1550 and 1150 BC, a cremation cemetery whose ashes were placed inside ceramic urns, evidence of Late Bronze Age cremation practices from the centuries that followed, and an Iron Age roundhouse with its own underground chamber, called a souterrain, from the first or second century AD. An earlier 2002 dig had found another Iron Age roundhouse nearby. The land was inhabited continuously through the centuries by people whose names and language were lost, replaced by Pictish in the early centuries CE, then by Gaelic, then by Scots. The Brandsbutt Stone on the outskirts of town - a class I Pictish symbol stone bearing an ogham inscription - is a fragment of that lost continuity, carved by people who were still here when the Romans gave up trying to conquer Scotland.

On the southern edge of the town rises a small flat-topped mound called the Bass of Inverurie. Tradition holds that it was raised by David, Earl of Huntingdon, brother of King Malcolm IV, in the late twelfth century - the motte of a Norman-style castle that has otherwise vanished. The religious foundation here is older. St Andrew's Parish Church, called in earlier centuries the Kirk of Rocharl, was founded by Culdee monks in the ninth century, putting Christian worship on this site for over a thousand years. The town's earliest written charter dates from 1558. Modern Inverurie began to grow only after 1806, when the Aberdeenshire Canal opened a barge route from Port Elphinstone to Aberdeen Harbour and the agricultural country of the Garioch finally had a cheap way to send its produce to market.

Three significant battles were fought in or near Inverurie. The first, in 1308, was the Battle of Inverurie - the climax of Robert Bruce's campaign against his Scottish enemies, the Comyns, after the earlier indecisive skirmish at Slioch the previous Christmas. The second, in 1411, was the Battle of Harlaw, fought just to the north between Donald of Islay, Lord of the Isles, and an army commanded by Alexander Stewart, Earl of Mar - a bloody draw that helped fix the political boundary between Gaelic and Lowland Scotland for centuries. The third, less commemorated, was a Jacobite skirmish in 1745. During the Second World War the Luftwaffe overflew the Garioch during raids on Aberdeen, but Inverurie itself was spared bombing. The town's history is much warred over and rarely bombed.

The Great North of Scotland Railway built its locomotive construction and repair works on a 15-acre site at Inverurie. The works opened in 1903 and closed in 1969, after carrying a generation of north-east men through the trades of steam engineering. Inverurie Locomotive Works F.C., the town's Highland League football team, still plays at Harlaw Park, named for the battlefield - a strange transmission of one history through another. International Paper ran a paper mill at Thainstone until March 2009. The 1970s North Sea oil boom brought a wave of new families and pushed the population steadily upward; the 2016 council survey counted 13,480 residents. JG Ross the bakers are headquartered here. Coombes, a small sweet shop, was famed as the oldest family-owned business in Scotland until its proprietor Colin Coombes died in 1957 and it closed with him.

On 15 October 2016, Inverurie was officially twinned with Bagneres-de-Bigorre, a Pyrenean spa town in southern France. The partnership has built school exchanges and ceilidhs, and the loss of Fiona Peebles in 2023 - the Scottish anchor of the twinning - was mourned in both towns. About five per cent of Inverurie's residents speak the Aberdeenshire Doric dialect of Scots primarily at home, and over half reported some proficiency in 2016. Names of distinction with Inverurie roots include the weaver poet William Thom, who lived here from 1838 to 1844; Hannah Miley, the Commonwealth Games swimmer; Peter Nicol, former world squash number one; the footballer Barry Robson; and the cross-country skier Callum Smith, who attended both the 2014 and 2018 Winter Olympics after passing through Kellands Primary and Inverurie Academy.