This question is from the Parenting Stack Exchange. I gave a brief answer there but provide more details here since the moderators often delete my answers. They also have a history of editing my content without indication.

NeutronStar says his daughter heard a strange noise coming from the toilet and has since been scared to use it by herself.

From the get go, he portrays her as emotional, calling her a “deeply feeling child”. That’s a sneaky way of saying ‘irrational’ – he avoids using that word but others know that’s what he means and in turn use that word in their responses. He complains:

[S]he started asking about if anything lives in the toilet and can come out while she is using it. We told her there is not.

He helped her one night but has decided to withdraw his assistance “so that this doesn't become a regular thing […]”. He’s just too inconvenienced.

Now that his daughter is traumatized and knows she cannot rely on her parents for help, NeutronStar wants to know: “How can we convince her to go to the bathroom by herself?” In other words: how do we get her to disregard her concern and follow our judgment instead of her own?

This, of course, is the wrong question to ask. Also, it is not true that nothing can come out of the toilet while she is using it. Rats, snakes, and other animals can and do sometimes emerge from toilets. The solution is to keep the toilet clean and to install a so-called ‘rat guard’, which allows only unidirectional flow of matter.

So NeutronStar is not only factually mistaken but his daughter’s fear is rational. As I write in my brief answer to him:

Your daughter is smarter than you think she is. She recognizes that, just because the proximate cause of the noise she heard [gurgling pipes after repairs] has gone, does not mean animals cannot emerge from the toilet. She is being logical and rational.

The way to address the situation is to take her seriously, do the research, agree that she is right that animals sometimes emerge from toilets, assure her the issue will be addressed, order a rat guard, install it in her presence, and show her how it works. The need for a clean toilet also presents a wonderful opportunity to teach her the importance of cleanliness as it will solve a problem she wants solved.

For posterity, my full answer to NeutronStar reads:

A quick search online would have disabused you of the misconception that animals cannot come out of the toilet:

• https://www.nuckolsplumbing.com/blog/2020/october/critters-that-can-crawl-out-of-your-toilet/
• https://lifehacker.com/how-often-do-snakes-rats-and-spiders-really-crawl-up-1848335336

Your daughter is smarter than you think she is. She recognizes that, just because the proximate cause of the noise she heard has gone, does not mean animals cannot emerge from the toilet. She is being logical and rational.

The second source suggests getting a rat guard. It restricts the flow of matter unidirectionally.

Take your daughter seriously, admit to her she was right and you were wrong, tell her you looked into it and that a rat guard might help. Ask her if she thinks that’d be a good idea. If so, order it and install it in her presence.

Keeping the toilet clean also helps keep critters away, so this presents a good opportunity to teach your daughter the importance of cleanliness: by showing her how it solves a problem she wants solved.