The 30-year-old joined the Seasiders during the 2023/24 season and accumulated 48 appearances, scoring on 14 occasions across his two years with the club.
He followed in the footsteps of Gary Liddle, taking up a coaching opportunity during a lengthy injury lay-off.
But with an opportunity arising elsewhere for the former EFL winger, Thomas had called time on his spell at the Towbar Express Stadium.
Whitby Town Manager, Gary Liddle, said: "I'd like to thank Nathan for his time with us both playing and coaching.
"He has now taken up an opportunity in a different part of the country which wouldn't make working with us viable anymore.
"We wish him the best of luck in his future career."