Police were called to RAF Fairford in Gloucestershire in the early hours of September 27 after a local farmer reported a group of men with several white vans engaged in "suspicious" activity.
The base had been used by US bombers to carry out strikes on Iran, but they were withdrawn on security grounds shortly after initial suspects were arrested.
In total, seven men were taken into police custody for questioning and all were released on bail earlier this month.
On Tuesday, the Crown Prosecution Service said Mohmed Abdulkarim and Nouman Essghir, both 24, had been charged under the National Security Act 2023.
Abdulkarim faces one count of assisting a foreign intelligence service while Essghir has been charged with entering a prohibited place for a purpose prejudicial to the UK.
Both men, from London, will appear at Westminster Magistrates' Court later on Tuesday.
The five other men arrested during the investigation remain on police bail.
Counter Terrorism Policing previously said it was "highly likely that there is Iranian state involvement" in the incident.
Iran has consistently denied being involved.
"We will continue to work closely with our partners as this complex investigation continues," CPS Special Crime and Counter Terrorism Division chief crown prosecutor Frank Ferguson said.
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