Isinbayeva, 34, was unable to defend her title after the Russian squad was hit with a blanket ban by the International Association of Athletics Federations (IAAF) over a state-sponsored doping scandal which rocked track and field.
In her manifesto for the election, Isinbayeva, one of the poster girls of the sport, claimed she wanted to be a "bridge" between the IOC and the athletes.
But she is also angry.
"I will never agree with the fact that they banned me, I will never forgive that.
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"What can I say to whoever will be the champion? They will be second by default."
Isinbayeva was one of four new members on the commission elected by fellow athletes on Thursday to stand for a total of eight years.
The others were German fencer Britta Heidemann, South Korean table tennis player Ryu Seug-min and Hungarian swimmer Daniel Gyurta from Hungary.
Only one Russian athlete eventually took part in the Rio track and field tournament. US-based Darya Klishina failed to make the final of the long jump.
When the entire Russian team was banned from Rio, Isinbayeva was scathing in her criticism, describing it as "funeral for athletics" and a "blatant political order".
IOC president Thomas Bach said he was looking forward to working with Isinbayeva and the three other new members.
"My congratulations go to the newly elected members of the IOC Athletes Commission. We are looking forward to working closely with them to further advance the Olympic Movement."
Heidemann was elected onto the commission with 1,603 votes, followed by Ryu with 1,544, Gyurta with 1,469 votes and Isinbayeva with 1,365.
A total of 5,185 athletes at the Olympic Village voted, said the IOC.