The presenter told viewers she had decided it is “time I stopped setting my alarm for 3.40 in the morning” as she revealed the news live on air on Tuesday.
“I have loved being part of it,” she said.
“Before anything else, I wanted to thank everybody who is watching for your loyalty and support over all those years.
“I will really miss it but it is time to stop that alarm early in the morning, and thank you for watching.”
Louise added in a BBC statement: “I will take so many memories with me, including reporting on the shock and anguish of the Manchester Arena bombing; starting a national conversation about Menopause; and the life-changing moment I took part in the Breakfast Christmas Cycling Challenge which inspired my ongoing passion for endurance sport, which I will continue when I leave.”
Later this year will mark 20 years since Louise presented her first edition of BBC Breakfast as a stand-in host.
She later replaced Sian Williams as a full-time member of the team when the programme moved from London to Salford in 2012.
Louise will host her last BBC Breakfast later this year.
Paying tribute to her, BBC Breakfast editor, Richard Frediani said: “Millions of viewers have regularly woken up with Louise for 20 years and welcomed her and BBC Breakfast into their homes.
“We will miss her brilliant journalism, good humour and boundless energy. She has been a tremendous BBC Breakfast colleague on and off screen and will always be a friend to the team.”