It includes images from photographers such as Mathew Brady and Alexander Gardner. The 3D images were created from the original glass-plate negatives held by the Library of Congress.
Matt Raymond, the library's former communications director, created the app and will donate the 3D images back to the library.
He says many familiar Civil War images have a different look in 3D. About 24 images are presented, along with pop-up commentary.
Other images from key Civil War battles and other events will be released later.
The app has been launched on iTunes and can be downloaded for $1.99.