The 58-year-old had three spells at the club as a player between 1983-94, totalling six seasons. He then became their youth coach. He took over as manager of the first team in January 2012.
Streich helped Freiburg get promoted again after their relegation in 2015, guiding them to seventh-place finish in 2017. Under him, Freiburg played in European competition four times and featured in their first German Cup final in 2021-22.
"Christian Streich is leaving SCF at the end of the season after 29 years of coaching," the club said on Instagram.
"This club is my life... It is with a very heavy heart that I can announce that I won't continue my job as Freiburg coach," Streich said in a video posted on the club's social media accounts.
"After twelve years, it's the right time to bring in new energy, new people, new opportunities. I believe the players need this new energy."
Freiburg are ninth in the Bundesliga and were knocked out of the Europa League last week after a 5-1 aggregate loss to West Ham in the last 16.
"I took a long time to reflect and discuss the decision, but I feel that after 29 years, now is the right time to make way for new impetus, new people and new opportunities," Streich, who grew up near Freiburg, said in a video on the club website.
"I have been able to enjoy hundreds of special moments and memories during my time. This club is my life and I'm extremely grateful for the close cooperation and support that I've been able to enjoy here."
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