The EU imposed an asset freeze and travel ban on governor Adib Mayaleh in 2012 and 2013 for his role in financially supporting President Bashar al-Assad in the bloody war which has cost some 190,000 dead.
But governor Mayaleh, who also has French nationality under the name Andre Mayard, appealed against the sanctions to the General Court of the European Union.
The General Court, second only to the European Court of Justice, dismissed his appeal, finding that the EU had acted properly in putting him on the sanctions list.
At the same time, it noted the "particularity relating to the fact that Mayaleh has dual Syrian and French nationality."
EU law does not require member states to bar entry to their own nationals, even if those people are "forbidden entry into, or transit through, the territory of the EU," the General Court said.
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"In response to a question from the Court, the French Government indicated that, as a French national... Mayaleh was allowed to travel to France.
"Consequently, the restrictive measures adopted against Mayaleh do not prevent him from visiting his family in France," it concluded.
The EU last month agreed to expand sanctions against Syria, adding 16 names and two entities to the blacklist for their role in a "brutal war" against their own people.
The announcement brought the total number of Syrians under EU sanctions to 211 and the number of entities to 63.
The EU separately maintains an oil embargo on Syria and curbs on financial transactions with the country.
The United Nations estimates that more than 191,000 people have died in Syria since a 2011 popular uprising against Assad turned into a bloody sectarian conflict which has also displaced millions and destroyed much of the country.