The 24-year-old made his Seasiders debut during last season's 3-2 victory over Atherton Collieries and signed a new contract with the club in summer 2024, establishing himself as a regular in Gary Liddle's starting line-ups.
Walker, who joined the Seasiders from West Auckland Town in the winter of 2023, is capped by England at Under-17, Under-18, Under-19 and Under-20 level.
He joins a Scarborough side currently sitting 14th in National League North and he could make his debut at home against Radcliffe on Tuesday night.
Everybody at Whitby Town wishes Stephen well for the future.