A row erupted when Western Isles Council wanted to close Carloway Primary and end first and second-year secondary education at Shawbost, both on Lewis.
The school at Shelibost on Harris was also part of row, but parents agreed to closure to end uncertainty.
In December 2011, ministers call the plans in and refused to agree to the closures. The council sought a judicial review, and in 2012 Lord Brailsford overturned the refusal of consent.
Last year the Scottish Government's appeal against the review failed and costs were awarded to the council. Now it has received a £72,000 settlement.
Council spokesman Nigel Scott said: "Settlement at this level means that the council has recovered over 80% of expenses due."