One reason could be a past bad experience. Maybe he had a really painful treatment as a kid that left a deep mark. For example, if he had a serious injury once and the doctor was rough while treating him, it would make him fear doctors.
Perhaps it has to do with the unknown. Naruto is used to facing known enemies on the battlefield, but doctors and their medical procedures are a mystery to him. He doesn't understand how they can poke and prod at him and it makes him scared.
It might be related to the intimidating environment of the hospital in the Naruto world. The cold, sterile look of the place and the smell of medicine could be overwhelming for Naruto. Also, seeing other patients in pain there could contribute to his fear.
He could start by getting to know a kind doctor. If he meets a doctor who is gentle and takes the time to explain things to him, like how a treatment will help rather than just doing it, it might ease his fear.
One reason could be the fear of losing his friends. Naruto has always been very protective of his comrades. In some fanfictions, he might face a situation where he is on the verge of losing them, like a powerful enemy threatening to kill them all. This would make him afraid as his friends are his most precious things.
In some fanfictions, Naruto might be afraid of doctors because of past traumas related to medical treatment. Maybe he had a bad experience during a recovery process, like a painful treatment that left a psychological mark.
He could start by having a positive experience with a kind doctor. For example, a doctor who takes the time to explain things to him gently and shows real concern for his well - being.
One possible reason could be that they had a past traumatic experience related to explosions. Maybe they witnessed an explosion that caused harm to their loved ones or themselves. Another reason might be that explosions in the 'Naruto' world are often associated with powerful and dangerous jutsus or attacks, and they are simply afraid of the destruction and chaos that explosions can bring.
One possible reason could be that his sister has some special or unknown powers that Naruto doesn't understand. For example, if she has a very unpredictable and potentially dangerous kekkei genkai. Another reason might be that she has a very strong and intimidating personality, which makes Naruto feel small and scared in her presence.
One possible reason could be past trauma. Maybe he had a bad experience in his childhood, like being bullied or physically hurt by someone. Another reason might be related to his magical abilities. He could be afraid that being touched might somehow disrupt his magic or cause an unexpected magical reaction.
It could be an old enemy who has come back with new and more terrifying powers. For instance, Orochimaru might return with some kind of jutsu that can directly target Naruto's mind and create unfathomable fears in him.
Maybe it's the high expectations that Naruto has for Boruto. Naruto is a hero, and he might unknowingly put a lot of pressure on Boruto to follow in his footsteps. Boruto could be scared of not being able to meet those expectations.
One possible reason could be that Kushina has a very strong and intimidating personality. In the Naruto universe, she was known to be a tough kunoichi. Naruto, who might be used to more gentle or reserved people around him, could be scared of her boldness.