Hafez Makhlouf, who heads Damascus' secret services, counts among the regime's hardliners, and is alleged to have been in charge of the brutal repression against demonstrators.
According to the Swiss court's ruling published on its website, Makhlouf had been contesting the sanctions imposed on him by Bern, arguing that the embargo was based on inaccurate information.
As part of his bid to contest Bern's actions, Makhlouf sought to travel to Switzerland to meet his lawyer, but the court turned down his request for a visa.
The court found that the Syrian and his lawyer had "at their disposal modern modes of communication" and the lawyer "can travel to Syria with ease" to meet his client.
Makhlouf figures in sixth position on a list of 54 people whose assets have been frozen by Bern, according to the court.
Makhlouf is "designated as the colonel in charge of the Damascus' unit in the intelligence command," it said. He is also "implicated in the repression against demonstrators."
Some 50 million francs ($53 million) in Syrian funds have been frozen by Switzerland. It is unclear how much of the sum belongs to Makhlouf.