Uzumaki Naruto is one of the strongest characters in the anime, if not the strongest. He is a jinchuriki of the nine tails and has perfected sage jutsu.
In addition to these abilities, Naruto also has very high chakra reserves and accelerated healing thanks to Kurama.
Uzumaki Nagato or Pain is one of the most difficult opponents Naruto had to face. He possessed the rinnegan and he destroyed the entirety of Konoha in a matter of minutes.
The six paths of Pain proved to be too much for even the legendary Sannin, Jiraiya to handle and he was defeated by Pain.
In a battle, however, Naruto would win against Pain. Pain is extremely strong and his Rinnegan grants him amazing abilities, but he still cannot defeat Naruto.
Naruto learned the Bijuu mode and got the six-path sage's chakra. This made him much stronger than he was when he first fought Pain.
In a battle, Naruto would be able to counter many of the attacks using his Bijuu mode and the truth seeker orbs. Madara, who was much stronger than Pain, was defeated by Naruto.
Naruto already managed to defeat Pain twice before he reached the peak of his power. This once again proves that Naruto is more powerful than Pain.