Scott was elected the first Member of the Scottish Parliament for Shetland in May 1999. He was also the first parliamentarian for the Shetland Islands as a distinct entity; up to that point there had only been a single UK parliamentary constituency for both Orkney and Shetland. He served as a Deputy Minister for Parliament in the Scottish Executive from 2000 to 2001 in succession to his colleague Iain Smith, but resigned after refusing to support the Executive in a vote in the Parliament on a tie-up scheme for fishing.