It is said the pair, a man and a woman, broke into the high security military base in Argyll and Bute, home to Britain's Trident submarines, at around 4am on Tuesday.
No details have been released on how long the pair were on the base, but they were detained by police and taken into custody after being discovered.
They are expected to appear at Dumbarton Sheriff Court today.
A spokeswoman for the Ministry of Defence said they were aware of the incident and were conducting an investigation.
The base has frequently been targeted by peace protesters and has been the site of a number of demonstrations in recent years.