A total of 1,600 hectares of ancient woodland overplanted with non-native trees or affected by invasive species such as Rhododendron ponticum will be "brought back from the brink" through the "once-in-a-lifetime project", the trust said.
It will work with environmental project management specialist RDI Associates and the woodlands' owners in two priority areas, the Great Glen and Three Firths, and the Cairngorms and Hinterland.
Peter Lowe from the Woodland Trust Scotland said: "Many of the ancient woodlands converted to plantations up until the 1980s are reaching economic maturity. It's time to think urgently about the future management of these plantations and how to unravel decades of decline by beginning a process of restoration.
"If this is not started soon the chance to restore the smothered ancient woodland will be lost forever."
Just one per cent of Scotland is covered by ancient woodland, while more than a third of conifer plantations in the 4,500 sq km Cairngorms National Park are on ancient woodland sites.
Its convener Duncan Bryden said: "Enhancing woodlands in the park is one of the key objectives in the Cairngorms Nature Action Plan, so we are delighted it has been chosen as one of the two project areas in Scotland."