It is suspected that the victim was bitten by a midge carrying the virus in eastern France where it had circulated among animals this northern hemisphere spring and summer, the government said in a statement.
The World Health Organisation said it was in contact with French authorities about the outbreak.
The patient died in early October and had been receiving treatment for a serious illness that made them more susceptible to infection than the general population, the Stockholm-based European Centre for Disease Prevention and Control said in a statement.
The victim was a man in 60s living in the Lyon area, local newspaper Le Progres reported.
"Based on current information and knowledge of the transmission of closely related viruses, this is an isolated human case and it is unlikely to lead to wider spread at this time," said the Geneva-based WHO, which co-ordinates responses to international public health issues and emergencies.
The French government also said no health risk to the general population had been identified.
Investigations are ongoing to clarify whether the virus caused or contributed to the French patient's death, the government said.
Authorities currently assume that the man was infected by a Culicoides midge in eastern France, an area where the Shamonda virus has been detected in animals.
Shamonda is transmitted by biting midges and most commonly found in cattle although it has also been found in horses, alpaca, sheep and goats, according to the World Organisation for Animal Health (WOAH).
It is not classified as a disease under the European Union Animal Health Law and not subject to official surveillance or control measures.
Identified in Nigeria in the mid-1960s, Shamonda was first confirmed in Europe in late July after genomic tests on sick cattle in southern Germany, Switzerland and eastern France.
The virus has circulated in Africa and Asia for decades but so far no case of human infection had been known, according to French authorities.
France's weekly animal health surveillance bulletin said it had also been detected in Austria, Belgium, Ireland, Italy, Liechtenstein, Luxembourg, the Netherlands, Portugal, Slovenia, Spain and the United Kingdom's Jersey.
The virus has several effects on animals,with affected cattle showing diarrhoea, weakness, loss of appetite and, less often, fever, French animal health authorities said.
A study of nine French dairy farms found milk production fell by up to 75 per cent.
with DPA
