The decision means French national champion Arnaud Démare will not be able to contest the expected sprint finish.
Groupama-FDJ did not reveal if the team member was a rider, only posting a brief message on social media.
"We won’t take part in Scheldeprijs on Wednesday after a positive test for COVID-19 by one of our team," Groupama-FDJ wrote.
The team entered for Scheldeprjis included Démare, Jacopo Guarnieri, Antoine Duchesne, Lewis Askey, Ramon Sinkeldam, Tobias Ludvigsson and Ignatas Konovalovas.
Groupama-FDJ are the second team to withdraw from the Belgian race after Trek-Segafredo announced on Monday that they would not race "as a precautionary measure" following the COVID-19 cases that forced them to miss Gent-Wevelgem last week and left several riders in isolation for several days.
The team rode Sunday’s Tour of Flanders but then wrapped up their cobbled Classics campaign.
"Due to the positive coronavirus cases detected last week we have decided to withdraw our men’s team from racing Scheldeprijs as a precautionary measure," Trek-Segafredo said in a statement.
"The team will isolate at home for a week for extra safety, before returning to competition at Brabantse Pijl."
Under the UCI medical protocol to ensure races can go ahead during the COVID-19 pandemic, riders and team staff are tested regularly before races and form a protective team bubble. Under a Belgian Cycling protocol, riders also undergo extra testing on the day before races.
The discovery of COVID-19 cases at Lotto Soudal, Trek-Segafredo and Bora-Hansgrohe before the recent Belgian Classics put the peloton on high alert in the countdown to the recent Tour of Flanders, with teams knowing that just one positive case could mean they would miss the biggest race of the spring.
Bora-Hansgrohe missed the E3 Saxo Bank Classic and Gent-Wevelgem after Britain’s Matt Walls tested positive for COVID-19. The COVID-19 race doctor ruled that 16 people were classified as ‘close contacts’ and so had to go into a seven-day quarantine. However, the team pushed for a review of the decision and the team were eventually allowed to ride the Tour of Flanders.
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