Isinbayeva was under pressure to quit as head of RUSADA's supervisory council after the World Anti-Doping Agency (WADA) called for her removal, one of four steps it said were necessary for RUSADA to retrieve its right to oversee the testing of Russian athletes.
"I will work and implement anti-doping programmes. I am simply transferring my seat to a new chairman," Interfax cited Isinbayeva as saying on Wednesday.
Isinbayeva added she would remain a member of RUSADA's supervisory council despite her resignation as chairwoman.
It was not immediately clear how WADA would respond to Wednesday's development.
RUSADA was stripped of its WADA accreditation after a report published in November 2015 accused it of systematically violating anti-doping regulations.
A majority of Russian athletes are set to miss the world championships in London in August if a separate but related ban against the country's athletics federation stays in place.
Other changes WADA is demanding from RUSADA include drug testers being allowed access to closed cities where it says athletes continue to evade testing, access to athletes' biological passports, and the implementation of a conflict of interest policy.
Isinbayeva's appointment last December outraged WADA because she was an outspoken critic of the decision by the International Association of Athletics Federations (IAAF) to ban Russian track and field athletes from international competition.
That decision kept the athletes, including Isinbayeva, from competing in the 2016 Olympics. Isinbayeva retired soon afterwards.
While formally banned, some Russian athletes hope to compete internationally as neutrals.
Fifteen athletes, including 2015 world champion hurdler Sergey Shubenkov, have so far been cleared to compete in international competitions after satisfying the IAAF's doping review board that they have been training in an environment that passes the necessary anti-doping requirements.
(Reporting by Moscow newsroom; Editing by Andrew Osborn and Pritha Sarkar)
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