"The Jordanian citizen ... arrested in Kenya, may not enter Swiss territory until further notice," said the Federal Justice Ministry in Bern in a statement.
"Clear evidence shows that he visited regions of Somalia where jihadist groups are involved in conflict (against the government). It also appears that he had contact with Islamist elements in Switzerland."
The refugee, 19-year-old Magd Najjar, was caught in May and charged in Nairobi on June 6th for links to Islamist Al-Shabaab rebels.
He now stands to lose his asylum status in Switzerland, since Swiss law states that this can be withdrawn if a refugee threatens or compromises national or international security.
The Al-Qaeda-linked Shabaab militants control large parts of southern Somalia, despite recent losses to African Union troops, government forces and Ethiopian soldiers.
Najjar as a student lived in Bienne, a small town close to the Swiss capital.
In recent years Switzerland has revoked the refugee status of between four and 29 individuals annually.
If this happens to Najjar, his only hope of returning to Switzerland is to appeal to highest court, the Federal Tribunal.