The McFly singer – who is currently on tour with the chart-topping band – and his professional partner tested positive following their performance in the first live show of the current series on Saturday night.
On Sunday afternoon, the BBC confirmed that Tom and Amy are now self-isolating, and therefore won’t be appearing in the second live show of the series.
However, they have been given a bye to week three, when they will hopefully be able to return to the competition.
A statement from the BBC said: “Tom Fletcher and Amy Dowden have tested positive for Covid-19. The pair are now self-isolating separately following the latest government guidelines.
“While they will both miss Saturday’s live show, Strictly Come Dancing protocols mean that all being well, they will return the following week.”
Posting on her Instagram following the announcement, Amy wrote: “Unfortunately Tom and I have tested positive for Covid-19. I’m not suffering any symptoms but am now isolating at home.
“I have no doubt that over the next 10 days my mind will be going crazy with choreography ideas ready to get back on the Strictly dance floor for the live show in week three!
“Thank you for all of the support and good luck to all of the couples this week. I will be cheering you all on!”
Earlier in the day, Tom was forced to pull out of a performance in Glasgow due to a then-undisclosed illness.
“Unfortunately Tom is unwell and won’t be onstage with us tonight in Glasgow,” McFly said in a statement.
“Tom sends huge and heartfelt apologies to all the fans he won’t see tonight. The show will still be going ahead, we’re looking forward to seeing you all and need you guys to sing extra loud for us tonight.”
A subsequent statement from the group said: “Further to our last message we can now confirm that Tom has tested positive for Covid-19.
“He is now self-isolating and following the latest government guidelines. Please join us in wishing him a speedy recovery.”
Tom and Amy were the first of this year’s Strictly couples to perform on Saturday night, earning 21 points from the judges for their Cha Cha Cha routine.
Strictly Come Dancing returns on Saturday night at 6.45pm on BBC One.