The story spans several locations within the manor, including:
* The house itself: This includes various rooms like bedrooms, a drawing-room, and a library.
* The gardens: These are vast and overgrown, with the hidden "secret garden" being the most significant location.
* The moors: The wild, open moorland surrounding the manor is another prominent setting.
While the exact town or village where Misselthwaite Manor is located is never explicitly stated, the descriptions of the landscape and the characters' activities suggest a rural setting in the Yorkshire countryside.