Misselthwaite manor in Yorkshire, England is a dreary place full of secrets and sadness. The biggest secret is that ten years ago Archibald's wife Lilly died in childbirth, leaving him with a son named Colin. Overcome by grief, Archibald locked up Lilly's favorite rose garden and buried the key. As time passed, ivy grew over the door, so that it is now completely covered. Archibald has also covered his heart, preferring to spend his time in Europe than with his son.

Orphaned by a cholera outbreak in Colonial India, a neglected and petulant child, Mary Lenox, is sent to live at the manor. Mary's arrival heralds change for Misselthwaite. With the help of a friendly robin, she finds first the key to the garden and eventually the door. As her new friend Dickon teaches her how to make the garden thrive again, Mary blooms from a sad child into a lovely young girl.

One rainy night she follows the sound of crying and discovers Colin, who has been raised to believe that he is sick and needs a wheelchair. Mary refuses to accept this diagnosis, and takes Colin into the secret garden, where he learns to walk. When Archibald returns from Europe and sees his son standing for the first time, he opens his arms and his heart, pledging to love and care for the children, and the garden, forever.