The 29-year-old, who works for a firm subcontracted by the energy giant EDF, had been granted access to nuclear installations as part of his job throughout 2012 and 2013.
But in March 2014 the man, who cannot be named according to French law, had his pass to enter the Nogent-sur-Seine nuclear power station revoked.
Officials said he had links with a jihadist terrorist group and that he was in touch with an imam involved in recruiting youngsters to fight in Iraq.
A court in the north-eastern town of Chalons-en-Champagne upheld the ban saying the management could prevent those "undergoing a process of political and religious radicalisation" from access to sensitive sites.
The lawyer for the man criticised the decision and argued that his client had no police record.
"There is no proof of these supposed links," said Sefen Guez Guez, adding that he might launch an appeal.
In June 2014, Guez Guez successfully had the ban revoked by an appeals court.
But when the engineer turned up for work, he found he was once again refused access to his place of work, this time by EDF, and his lawyer appealed again.
It is estimated that France is home to some five million Muslims, the largest population in western Europe.
Like some other European countries, France has expressed concern over radicalised young people leaving the country to fight in Iraq and Syria, who could pose a risk to domestic security on their return.
According to official estimates, around 800 French nationals or residents, including several dozen women, have travelled to Syria, returned from the conflict-ridden country or plan to go there.