One way is through his brute strength. Naruto is very powerful and he can simply overpower Neji in a physical confrontation. He can block Neji's Gentle Fist attacks with his own strength and speed.
Naruto might also use his strategic mind. He could analyze Neji's fighting style and find its weaknesses. Then, he would use this knowledge to prevent Neji from getting close to Hinata. For example, if he knows that Neji has a blind spot in his defense, Naruto would position himself and Hinata in a way that Neji can't easily reach them.
Another way is by using his friendship network. Naruto has many friends who are also powerful. He could call on them for help if Neji becomes too much of a threat. But more often than not, Naruto would take it upon himself to protect Hinata. His love for Hinata would fuel his determination, and he'd be like a shield, always ready to take any hit meant for her.