James Stewart from the village of Rothes was a grain merchant and also the owner of a mill. In 1868, he partnered with Robert Dick, William Grant (an agent of the Clydesdale Bank), and John Cruickshank (a lawyer) to take over the nearby Macallan distillery. The distillery operated successfully, and three years later they decided to build a larger distillery upstream in Rothes. However, this was not a good time to build a distillery. In the autumn of 1878, Britain experienced "the most severe economic crisis in a century": the City of Glasgow Bank collapsed in October, and the Clydesdale Bank followed suit in December. James Stewart and his partners dissolved their partnership; Stewart retained Macallan, while the others took over the half-built Glenrothes-Glenlivet distillery, continuing operations under the name William Grant & Company. The distillery's opening date was December 28, 1879—the night of the Tay Bridge disaster (see Balmenach)—with Robertson & Baxter as agents. Later, in 1887, following the advice of W.A. Robertson, Glenrothes merged with Bunnahabhain to form Highland Distilleries Company. In 1896, the distillery expanded according to the design of Charles Doig of Elgin, adding four stills and a second malt kiln. However, before the project was completed, a major fire destroyed most of the distillery. Despite the installation of Doig's patented equipment that prevented the new mill from exploding, the distillery could not avoid another fire six years later. Glenrothes expanded to six stills in 1963, increased to eight in 1980, and was rebuilt and expanded to ten stills in 1989. In 1987, Highland Distilleries licensed the Glenrothes brand to Berry Brothers & Rudd, a London-based wine merchant that also owned 50% of Cutty Sark (the other 50% was held by Robertson & Baxter). That same year, they released the distillery's first official bottling: Glenrothes 12 Year Old. In 2010, the Edrington Group (owner of Robertson & Baxter) acquired 100% ownership of Cutty Sark, while Berry Brothers & Rudd obtained 100% ownership of Glenrothes. However, in 2017, the situation reversed, and the Glenrothes brand returned to the Edrington Group, with plans to increase the brand's influence in international markets. Until 1994, the distillery's name was Glen Rothes; it was changed to Glenrothes thereafter.

Due to The Glenlivet's immense prestige, 27 Speyside distilleries appended 'Glenlivet' as a suffix to their names. In 1884, John Gordon Smith sought to restrict this practice. Before it reached court, the owners of Glenlivet, Cragganmore, Mortlach, Glenfarclas, Linkwood, Glen Grant, Glenlossie, and Benrinnes reached an agreement: Smith's distillery would be named The Glenlivet, while they could hyphenate 'Glenlivet' to their distillery names and market their vatted malt as vatted Glenlivet. Others soon followed suit. Andrew Usher was granted exclusive rights to continue selling Old Vatted Glenlivet. The distillery draws its process water from a spring that was allegedly the site of a 13th-century murder. According to legend, Lord Ross's daughter Mary Leslie was slain by the notorious 'Wolf of Badenoch' (Alexander Stewart, Earl of Buchan) while protecting her lover. In addition to a new label design in 1994, Glenlivet also adopted a unique bottle shape for filling, affectionately dubbed 'La Bomba'. In 2005, they launched 'La Bombette', a hand-grenade-sized 10cl miniature bottle available in two versions.