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Jenner, 71, sparked controversy and backlash online for staunchly opposing the idea of "biological boys who are trans competing in girls' sports in school."
The former Olympian's comments follow on from several US states pushing forward with bans on transgender girls' participation in girls' sports.
Rapinoe, who has been a vocal champion on LGBT issues and equal pay for women, previously claimed that sports have been used as "another avenue to attack" trans rights.
And the 35-year-old US international has hit out at Jenner over her trans comments, saying that she is "not an exceptional politician."
Rapinoe told Fubo Sports Network's The Cooligans: "You were an exceptional athlete. You're not an exceptional politician."
Jenner has announced her intention to run for governor in the US state of California, saying in a statement that "Sacramento needs an honest leader with a clear vision."
However, the American reality TV star has since doubled down on her views towards trans girls being banned from competing in girls' sports.
Speaking to Fox News this month, Jenner said: "I stick with my statements that I made [...] I think we have to make sure that the integrity of girls' sports is there, I think that's extremely important.
"But there's more to it than just what I said, because I just said 'biological boys in sports' -- there's more to it than that, and I think in the future I will explain more of that."
One doctor has since slammed Jenner's remarks by claiming that there is no current evidence that trans girls would perform better in sports than cisgender girls.
Rapinoe has campaigned for equal pay for women in football and even visited the White House in March as she delivered a powerful speech in front of US President Joe Biden.
However, the 2019 Women's Ballon d'Or winner is unsure of venturing into politics after her career in football.
"It takes a ton of skill and institutional knowledge," Rapinoe admitted.
"Those people are talented politicians. I think people need to think of it that way. They actually have a talent for doing the politicking.
"I love talking about politics from my perspective, from my lane. I honestly think it's become too much of a popularity [contest].
"I probably could be a representative of some kind, win a district here or there, but am I really the best person to be doing that?
"Maybe I can just talk about the person who is actually the best person to be doing that."
Laughing at the idea of running for president of the US, Rapinoe added: "Unless it's the president, and then probably, I'll just do it."
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