The distillery was built in 1968, adjacent to the original Clynelish distillery which was closed. Confusingly the original distillery was reopened in May 1969 and until July 1973 produced a heavily peated whisky to supply for blending; this was done to cover a shortage of Islay whisky caused by a drought on the island. The old distillery was renamed Brora Distillery and production of a peated spirit continued up until 1983.
Clynelish has had a strong connection with Johnnie Walker blended whisky for many years. A large proportion of the spirit used in Johnnie Walker Gold Label Reserve comes from this distillery.