I was going to say Aralé from Dr. Slump when I read again the title and realized she doesn't fit the criteria. Haha.
She's an innocent looking child, but in reality she is a robot made by Dr. Slump, which is why she'd just be a few days old.
I know Goku looks young in dragonball but I think he was actually 14 years old despite the art style...I'm not sure. I think I'd have to research to confirm this.
Gohan was originally going to be tje main hero in dragonball Z, and he was shown first when he was something like 4 years old, but since in the end Goku stayed in the spotlight, I guess it is subjective if you want to count him as a protagonist and thetefore if he qualifies or not as the youngest human anime protagonist.
And while I'm at it and I remembered, isn't Ash Ketchum like 9 years old when he starts his journey?