The appeal ruling stemmed from motions filed by one private individual and a number of nature protection organisations seeking to block construction at two possible sites, one at Simo and the other at Pyhäjoki, both in the north, near the country's west coast.
Fennovoima had already previously announced that it would inform local authorities of its decision on a location within a few weeks of a court ruling in the case.
Interviewed by YLE on Wednesday, Fennovoima CEO Tapio Saarenpää was not yet able to say which location will be the site of a new nuclear facility.
"Of course, I'm pleased that a decision was made and that we can now choose between two good sites," said Saarenpää.
The Pro Hanhikivi organisation, which opposes the construction of a nuclear plant in Pyhäjoki, expressed its disappointment with the ruling. It says that power lines from a projected plant would interfere with a main bird migration route and construction would destroy already threatened natural areas. The group says that if needed, it will file an appeal against the project with the EU Parliament.
Plant construction will still require permits conforming to legislation on nuclear power, environmental impact and construction standards. All of these will be open to appeal processes.
The Finnish parliament last year voted to back the building of two new nuclear plants, one by Fennovoima and the other by the utility Teollisuuden Voima, raising Finland's total number of power generating reactors to seven.
Fennovoima plans call for a start to construction in 2015, with completion in 2020.