The statistics give detail on the expenditure for administering the vote, including running polling stations across the country and issuing postal votes.
Scotland voted by 62% to 38% to stay within the EU, with all 32 council areas voting to remain.
The Electoral Commission calculates the cost per vote in Scotland was £3.66 - with a total of 2,681,179 people voting, adding up to a total of around £9.8 million.
Regional counting officers’ expenses for Scotland added up to £43,766.05 - a total that amounted to £27.95 over its funding allocation.
The total UK cost of delivering the vote on the EU in June 2016 totalled around £130 million.
The Electoral Commission will submit its recommendations on spending to the Cabinet Office to be considered for future elections.
Asked whether Prime Minister Theresa May regarded the cost of staging the referendum as good value for money, a Downing Street spokeswoman said: “The decision to hold a referendum was taken by the previous government.
“What is important now is that we are focused on delivering the result.”