Kent Police detained the two suspects, aged 22 and 20, at Dover Eastern Docks in the early hours of Sunday.
They are being held under Section 5 of the Terrorism Act 2006, on suspicion of preparing terrorist acts.
A spokesman for the South East Counter Terrorism Unit said the arrests were not linked to Friday's attacks in Paris, which left 129 people dead.
Two men have been arrested on suspicion of terrorism offences as they attempted to leave the UK via Dover.