Thomas (pictured) has been Head of Recruitment at Oxford United since 2014, and will take on the same role at Derby County.
Derby have been searching for a Head of Recruitment since October 2022, five months after Joe McClaren left the club.
Oxford praised Thomas for "building a modern recruitment department."
Thomas said: "It has been challenging, but I am very grateful to the club for providing me with the opportunity to design and implement a recruitment structure and strategy I believe in. I am extremely proud of the work we have done together over the past nine seasons; developing young players and seeing the club grow and push for promotion.
"However, it’s now time for a new challenge, and the chance to join a huge club like Derby was too exciting to turn down. I know I am leaving a club that has extremely exciting plans and I leave on the best of terms, wishing everyone the best of luck for the future."
Meanwhile, Newport County, one division lower, are on the lookout for a new Sporting Director following Kelly's exit.
He had been in the job since June 2021, but has left "for a new opportunity closer to home," the club said.
Newport are level on points this season with Crewe Alexandra, a club which has found success in the loan market on TransferRoom in recent months, as explained by their Head of Recruitment Josh Kennard in an interview that can be watched here.
Picture credit: Oxford United
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