As the leader of Akatsuki and one of the two sides of the Amegakure Civil War, Pain is an extraordinarily powerful ninja that can easily be considered Kage-level; his partner Konan has stated that he has never lost a fight. He was able to single-handedly defeat and overthrow the former Amegakure leader, Hanzō, and made short work of Jiraiya after unveiling all six of his bodies (though Pain admitted that killing Jiraiya would have been very unlikely had Jiraiya had prior knowledge of his six separate bodies).
Pain has been seen using many highly advanced techniques like the Shapeshifting Technique, which allows him to clone Akatsuki members using human sacrifices that they control and can use to engage enemies in place of themselves. The clones formed are perfect copies of the original, possessing any unique genetic traits or weapons they may possess. The clone's abilities are proportionate to the amount of chakra given to the clone.
His most important technique in regards to Akatsuki operations is the Illusionary Dragon Nine Consuming Seals. With the other members of Akatsuki, this technique begins a three day trial to forcibly extract the Tailed Beast from its host and forces it into a giant statue. There seems to be a order on which Tailed Beast they can seal at once as they are unable to seal the Nine-Tailed Fox without sealing the other beasts as it would destroy the statue, possibly freeing all the captured beasts.
It also enhances his vision in a similar manner to the Hyuga's Byakugan, allowing him to see through solid objects and sense the chakra of barrier techniques as well as give tremendous analytical powers like the Uchiha's Sharingan.