Portions of several structures were used to depict Misselthwaite Manor. The exterior is primarily 16th-century Fountains Hall in Yorkshire and some of Allerton House in Yorkshire. The kitchen set was built in a classroom at Eton College. Lord Craven's study is at Harrow School. The main staircase was in St. Pancras Chambers, adjoining the busy St. Pancras Station in Central London. The bedroom interiors were shot on sets on 'A' stage at Pinewood Studios. The grounds were shot in Allerton Park in North Yorkshire and some of Luton Hoo in Hertfordshire as well as Pinewood Studios in Buckinghamshire. The topiary arch used for the Misselthwaite garden leads directly onto Conistone Moor in North Yorkshire.
The tapestries in Mary's room comprise a cycle known as "The Hunt for the Unicorn". In this cycle, the unicorn is lured from the wild and into a new life by a young virgin, foreshadowing Mary's role in the story.
The biggest challenge for production designer, Stuart Craig, was the garden. The garden was built from scratch to avoid the logistical nightmare of crowd control that would have been required for a complicated summer/winter shoot in an existing garden.
The costume design is so detailed that the initials "M.L." (Mary Lennox) can be seen embroidered on Mary's stockings for the split second they appear on-screen, while Mary's Ayah is dressing her (at around 1 min), at the top of her thigh length white stockings.