The museum honours the famous regiment which was amalgamated in 1994 to become part of the Highlanders, with Prince Charles its last colonel-in-chief.
It has seen business from energy firms suffer amid the oil price downturn.
The museum relies heavily on income from oil and gas firms, for events such as conferences, training days and dinners.
The award-winning attraction - which celebrates its 20th anniversary this year - has suffered an 80% drop in profits, despite a rise in visitor numbers, and tours last year which involved children from more than 50 schools.
The museum said it needed to raise £100,000 a year for the next three years to keep it going.
An official campaign will be launched next week.
The museum re-opened in 2006 after a £1.2m refurbishment.
The Gordon Highlanders Museum in Aberdeen could face closure if it cannot raise funds, it has been warned.