I guess it is kind of normal for not having really played for a long time. From what I read, and know, you’re probably applying too much pressure to your thumb on the neck (assuming we’re talking about your fretting hand). I used to have the same problem from what I can remember usually and especially during barre chords. Either way, I recommend warming up before you start practicing or playing. We tend to overlook warm ups, but it could help. If you’re hurting, try warming up, and applying less pressure to your thumb. If it has anything to do with barre chords, take a break from doing those every once in a while.
You know, what? I do remember having that problem and mine was because of the way I had my hand positioned (warming up the right way will help you eventually), but yeah it was from having to stretch because I was learning new things, and I’d have to stop playing for like a day or hours because my thumb for some reason hurt, but it went away after a while because my hands got used to the stretches and what have you. It could be that, so it goes away.