Fort George in Inverness-shire, which narrowly avoided closure in a previous round of cuts in 2011, could be among the casualties as the MoD looks to rationalise its property portfolio across the UK.
The department plans to reduce its footprint by 30 per cent with profits from sell-offs reinvested back into the Armed Forces.
There are around 120 military sites in Scotland, including Reserve centres.
These include major bases housing critical UK military capabilities and other essential facilities, such as HMNB Clyde and RAF Lossiemouth, to the outdoor training facility at Kirkcudbright.
The MOD said as of April 1 it owned 220,000 hectares of land in the UK and had rights over a further 204,000 hectares - 1.8 per cent of the UK’s landmass.
Around 36 per cent of the MoD’s estate is in Scotland. It employs 10,320 military personnel and 3,800 civilian north of the Border.
A spokeswoman for the MoD said its commitment to reduce its landholdings was “a long-term, detailed piece of work which more appropriately meets the needs of our Armed Forces by being of better quality, more cost effective and more efficient by 2040”.
A final decision on which bases will be closed as part of this strategy is expected later this year.
But residents living close to Fort George, 11 miles north-east of Inverness, are already campaigning for the historic garrison to be spared.
Built in response to the 1745 Jacobite rebellion, the fort has continuously housed troops since 1757.
In 2007 it became the new garrison of the Black Watch.
Drew Hendry, MP for Inverness, Nairn, Badenoch and Strathspey, said the base was estimated to be worth around £16 million a year to his constituency.
“It makes an enormous economic impact in the area,” he said.
“I went round the doors with a petition to save the fort last week. It is fair to say people are hugely concerned.
“People in Ardersier were snatching the petition out of my hands to sign it.”
A spokeswoman for the MoD said no decision has been made on the future of Fort George.
She added: “The MoD will engage with all impacted parties at the appropriate time on the future of any Scottish site. This will include writing to Secretary of State for Scotland along with the constituent MPs and MSPs to inform them of the department’s position.”
The only site north of the border so far confirmed as surplus to requirements is the Craigiehall estate near Edinburgh, which served as the British Army command headquarters in Scotland until 2014.
Plans were unveiled in February which, if approved, would see 1200 homes and a transport hub built on the land close to Cramond.
A further 21 sites across England and Wales have been earmarked for closure. The majority will be sold for housing development.
The spokeswoman added: “The estate optimisation strategy aims to provide a more efficient and better quality Defence estate to support our Armed Forces, which will be fit for purpose for future generations.
“It will better support military capability and force generation by allowing the formation of clusters of sites to collocate similar functions, therefore reducing running costs. It enables the disposal of under-used sites for which there is no longer an enduring Defence requirement and will provide significantly better facilities to support the men and women of our Armed Forces.
“No decisions about the future of individual sites, other than those already announced in January and March of 2016, have been made at this point. The MoD expects to announce the full strategy later this year.”