Thomas is Wrexham-born and was a regular with the U21 team last season.
He told evertonfc.com: "The emotions are very high – obviously being at the Club for 11 years to being offered a first professional contract here is massive.
"It shows the hard work I've put in, but also that my family have put in. It's all been worth it. Having my family here and having my picture taken with them is definitely a memory we'll all cherish and look back on in a few years.
"After last season, working a lot with Taity (Paul Tait, U21 coach), I'm looking forward to working with him again. It's just about keeping my position, getting in as many minutes as possible and pushing to get to the other end of the Finch Farm building with the first team as much as possible.
"That's obviously where I want to be, training with the first team and being around those players. They're the ones who are best to learn from."