Russian sports bosses agreed earlier this month that Isinbayeva would leave in line with a request from the World Anti-Doping Agency (WADA), one of a raft of criteria the country needs to fulfill in order to get its drug-testing body RUSADA reinstated.
Press reports, however, said that Isinbayeva would remain as a member of RUSADA's supervisory board.
RUSADA has been suspended since 2015 in the wake of the report by Richard McLaren which uncovered widespread doping in Russian sport.
As she stepped down the two-time Olympic champion said RUSADA appeared on course for "interim reinstatement" this month in a move that would see it start to test its own athletes again.
"I'm happy that I've achieved my goal. I know that now I need to make way for a new chairman who will complete RUSADA's full reinstatement," she was reported as saying by Interfax news agency.
Isinbayeva added that Alexander Ivlev, the deputy chairman of RUSADA's supervisory board, will be appointed as its new boss in near future.
Russia's Deputy Prime Minister Vitaly Mutko, who oversees sport, replied that the country will comply with all of WADA's demands.
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