Could be the way your action is set up on your guitar, or it could be poor positioning.

Take a small ball (like one of those bouncy rubber ones that children play with and like to throw at walls and dogs and stuff), and sit it in the palm of your hand. Then try to hold the neck of your guitar with the ball still in the palm of your hand. That's pretty much the grip you should typically have while playing guitar. Your thumb should always be placed in the middle of the next and it'll usually be found facing your index and middle finger right in between them. Your hands take time to get used to it if you're new to playing as you know, but this should be much more comfortable if you weren't playing like this before. Hope this makes sense and hope it helps. Cheers!