His departure follows lengthy criticism of his stewardship of the company, which has seen its share price collapse to about $10.
Earlier in the year he fought off a hostile takeover bid from Microsoft which offered $33 a share.
Mr Yang also told the workforce that he would be participating in the search for his successor.
"I will always do what is right for this great company," Mr Yang wrote in an e-mail to employees
The BBC was told that Mr Yang made the decision to leave as chief executive officer last month. No names were given as to who will succeed him.
The company, based in Sunnyvale, California, said it is interviewing candidates inside and outside Yahoo in a search led by chairman Roy Bostock.
"Jerry and the board have had an ongoing dialogue about succession timing, and we all agree that now is the right time to make the transition to a new CEO who can take the company to the next level," said Mr Bostock.
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