Nagelsmann, who is fully vaccinated, missed Bayern’s 4-0 win over Benfica in the Champions League on Wednesday after developing symptoms while in Portugal.
The 34-year-old coach will return from Lisbon separately from the team and will self-isolate upon arriving in Germany.
Bayern host Hoffenheim in the Bundesliga on Saturday before they face Borussia Monchengladbach in the second round of the German cup on Wednesday.
The Bundesliga champions sit top of the table following their 5-1 destruction of Bayer Leverkusen at the weekend, who came into the match second to Bayern in the standings.
With Nagelsmann absent from the touchline at the Estadio de Luz on Wednesday, Bayern continued their 100 per cent start to the Champions League group stage following Robert Lewandowski’s strike and a double from Leroy Sane.
A statement from Bayern said: “Despite being fully vaccinated, Julian Nagelsmann, 34, head coach of FC Bayern Munich, has tested positive for Covid-19. He is returning to Munich separately from the team by air ambulance and will self-isolate at home.”
The club said before the Benfica match that Nagelsmann had remained in the team hotel due to a “flu-like infection”.
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies