Mystery Stone may refer to:
- The Bourne Stone in Massachusetts
- Grave Creek Stone of Moundsville, West Virginia
- The Heavener, Poteau, and Shawnee runestones of Oklahoma.
- The Ica stones of South America
- Kensington Runestone of Kensington, Minnesota
- Los Lunas Decalogue Stone of Los Lunas, New Mexico
- Lake Winnipesaukee mystery stone of New Hampshire
- Runestone of Nomans Land, Massachusetts
- Stone spheres of Costa Rica