The 20-year-old Chelsea midfielder will therefore isolate for a period of 10 days and will miss Scotland’s final group fixture against Croatia on Tuesday.
Gilmour earned rave reviews last Friday when he was named man-of-the-match on his first ever start for his country as Scotland held England to a 0-0 draw in their second group game at Wembley.
The news will come as a huge blow to Scotland manager Steve Clarke, who will be hoping to get a positive result against the 2018 World Cup losing finalists to make the knockout rounds of the competition.
Scotland lost their first game 2-0 to the Czech Republic before earning a point against Gareth Southgate’s men.
"The Scottish FA can confirm that a member of the Scotland national team playing squad, Billy Gilmour, has tested positive for Covid-19," the official SFA statement reads.
"Having liaised with Public Health England since the positive test was recorded, Billy will now self-isolate for 10 days and therefore miss tomorrow’s UEFA Euro 2020 Group D match against Croatia at Hampden."
Gilmour has won three caps for the Scotland national team and was part of the Chelsea side that recently won the UEFA Champions League.