The proposed Stronelairg wind farm will be developed by SSE Renewables on the Garrogie estate near Fort Augustus in the Highland Council area.
At the same time, an application to build the 21-turbine Newfield wind farm, with a maximum generating capacity of 63MW and located near Lockerbie, in Dumfries and Galloway, has been refused on the grounds of unacceptable adverse visual, landscape and cumulative impacts.
Energy minister Fergus Ewing said the Stronelairg development will help "keep the lights on across our islands at a time where there is an increasingly tight gap between electricity supply and demand".
But conservationists are concerned about the impact it will have on Scotland's natural beauty.
Mr Ewing said: "The Stronelairg wind farm will create jobs both in its construction and during its lifetime."
But Helen McDade, head of policy for wild land conservationist the John Muir Trust, said: "This development flies in the face of advice from Scottish Natural Heritage, which objected to the development on the grounds that it would destroy the character of one of Scotland's key areas of wild land.
"SSE is a powerful multinational company with its HQ in Scotland and we know this project is worth many hundreds of millions to its shareholders.
"It is unfortunate that SSE's views seem to hold greater sway over ministers than the opinions of the Scottish Government's own expert body on the natural environment."
David Gibson, chief officer for the Mountaineering Council of Scotland, said it will be "a massively intrusive industrial development. The Scottish Government appears to be oblivious to the adverse impacts of such developments on tourism.
"Even studies sponsored by the renewables industry show a worrying trend."