The Ministry of the Defence (MoD) has had a tracking station on the isle since 1957.
It is linked to a missile range controlled from a military site on Benbecula in the Western Isles.
The National Trust for Scotland, which manages St Kilda along with the MoD, said the planned new buildings were "sympathetic and sustainable".
St Kilda lies about 40 miles (64km) west of North Uist, the nearest inhabited place to the archipelago.
The last islanders left St Kilda in 1930 and people only now live on Hirta on a temporary basis to work at the military site, or on wildlife conservation projects.
The MoD, working with its defence contractors QinetiQ and Skye-based architects Wittets, has submitted a planning application to Western Isles local authority, Comhairle nan Eilean Siar, for a redevelopment and environmental upgrading of its 50-year-old St Kilda facilities.
Galliford Try International and Hugh Broughton Architects have been appointed to develop the design of the new buildings.
NTS said the firms would be using expertise gained through building similar facilities in environments with challenging climates, including work for the British Antarctic Survey.
Lower parts of the new buildings would be "curtained" with stone walls designed to blend into the St Kildan landscape.
Wood panelling over the exterior walls will attain colours through weathering that will complement the surrounding scenery and roofs will be planted with native St Kildan grasses, said NTS.
Susan Bain, the trust's property manager for St Kilda, said: "We have been very impressed by the extent to which the MoD and its partners have gone to make sure they come up with proposals that will enhance the existing site and are both sympathetic and sustainable in the vitally important context of St Kilda.
"Most traces of the buildings from the 1960s will be removed and their replacements will be entirely appropriate to the setting in terms of design profile and best environmental practice.
"Every detail has been considered, down to ensuring that there is no chance of contaminant flora or fauna from the mainland being brought to St Kilda during the construction phase."
She added: "The military has a long association with St Kilda going back to the First World War and we are very pleased to have worked in partnership with the MoD since 1957.
"This has been entirely beneficial to our conservation activities on St Kilda and we look forward to this relationship continuing well into the future."
New military facilities are to be built on the island of Hirta in the remote St Kilda archipelago.