Steve Sankey was elected in the East Mainland, South Ronaldsay and Burray ward of Orkney Islands Council.
Party co-leader Patrick Harvie tweeted that he was "delighted" with the first Green gain in the elections, and the party's first Orkney councillor.
Robbie McGregor won the uncontested Shetland South seat for the SNP.
He is the first councillor to represent the party on Shetland Islands Council.
The Greens said Mr Sankey was the first member of a mainstream national party to be elected to Orkney Islands Council, where candidates have traditionally stood as independents.
Both Orkney and Shetland councils were independent holds.
Orkney has elected its first ever Scottish Greens councillor, while the SNP has gained its first representative in Shetland.