Bates, 37, joined the Seasiders as Assistant to Nathan Haslam in September 2022 having made his first venture into football coaching as Caretaker Manager at Hartlepool United in 2017.
The experienced former Middlesbrough defender made 225 EFL appearances, also representing Darlington, Ipswich Town, Norwich City, Bristol City, Bradford City and Hartlepool.
Bates departs the Towbar Express Stadium with the best wishes of everyone at Whitby Town as he takes up a new career path.
Town boss Haslam said: "Batesy has been brilliant for us. The last season was a very successful one for us and he was a major part of that success.
"He goes with my best wishes as he embarks on an exciting new role in football."