Passed last month, the law requires people to use the public toilet designated to the biological sex they were designated at birth, rather than the gender they identify with.
Meanwhile, a new law approved in Mississippi allows businesses to deny services to same-sex couples on religious grounds.
"I've spent a lot of time thinking about what kind of message these harmful bills send, especially to transgender youth growing up in these states," Jenner wrote in a lengthy blog post on her website.
"We all want safety and privacy in public bathrooms. But these anti-LGBT bills, like the ones in North Carolina and Mississippi, actually make us less safe, not more safe," the reality TV star and activist added.
"They open the door to abuse, aggressive and confrontational behavior in bathrooms, and encourage strangers to demand that women and girls prove that they are actually female in order to use the restroom. No one wants that."
Jenner, who shared the blog post with her 3.8m million Twitter followers, also urged people to "listen to the stories of actual transgender people who live near you".
"We have already seen the difference it makes!" she explained. "In South Dakota, a group of incredibly brave trans youth shared their stories with Governor Dennis Daugaard, and he vetoed a bad bill that targeted trans people."
During his visit to the UK, President Barack Obama said the controversial bill was "wrong" and should be overturned.
The British Government has changed its travel advice to warn of the impact on the legislation on LGBT travellers visiting the state.
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