"I have had the great honor of serving as this foundation's chairman for the last five years and its mission and success are my top priorities. Today therefore, to spare the foundation any negative effects as a result of controversy surrounding my cycling career, I will conclude my chairmanship," Armstrong said in a statement.
The move comes a week after the U.S. Anti-Doping Agency released a report detailing allegations of widespread doping by Armstrong and his teams when he won the Tour de France seven consecutive times from 1999 to 2005.
On the tail of Armstrong's announcement Wednesday, Nike also announced that it has ended its contract with the cyclist.
"Due to the seemingly insurmountable evidence that Lance Armstrong participated in doping and misled Nike for more than a decade, it is with great sadness that we have terminated our contract with him," the company said in a statement. "Nike does not condone the use of illegal performance enhancing drugs in any manner."
Armstrong will stay on the Lance Armstrong Foundation's 15-member board. Vice Chairman Jeff Garvey will take over Armstrong's duties as chairman. Nike said it will still continue to support Livestrong's initiatives.
The USADA banned Armstrong from cycling for life and ordered 14 years of his career results erased - including his seven Tour titles. The agency's report contained sworn statements from 26 witnesses, including 11 former teammates. Armstrong denies doping, but did not fight the allegations through arbitration.
The Associated Press contributed to this report.