Malik Mahmud, considered by the Free Aceh Movement (GAM) as its prime minister, and Zaini Abd Allah, the group's foreign minister, were detained for a few days in June 2004 on charges of breaking international laws by directing the armed struggle from afar.
They were freed pending a criminal investigation, but the charges were dropped in April. Abd Allah, whose group is now holding peace talks with Indonesia, said he had won compensation on Monday.
"It is about 10,000 crowns ($1,258)," he said. Sargon Debasso of law firm Althin, which represented Abd Allah, said the amount was slightly higher than normal given the fact the arrests received wide media coverage. "It is for psychological suffering," Debasso said.
He said people who were detained in Sweden but then not charged often had a good chance of winning compensation.
A spokesman for the movement said he did not know if Mahmud had also sought compensation.
GAM and Indonesia launched peace talks after Aceh took the brunt of the 26 December tsunami, in which nearly 130,000 people in the province lost their lives and more than 500,000 became homeless. A fifth round of talks is due to begin on 12 July.
The GAM leadership fled to asylum in Sweden after declaring independence from Indonesia in 1976. But jungle fighters stayed on in the devoutly Muslim province to combat Indonesian troops and some 12,000 people, mostly civilians, have been killed.