A method to obtain a nano-area electron diffraction pattern in transmission electron microscopy (TEM) was proposed, based on three-dimensional (3D)) image formation theory. This method allows us to reconstruct an electron diffraction pattern from a 3D Fourier spectrum of high-resolution through-focus images. As a test case, an electron diffraction pattern from a tilted Si single crystal was reconstructed using the proposed method and compared with the conventional selected-area electron diffraction pattern. The intensity distribution of the reconstructed electron diffraction pattern was confirmed to be qualitatively equal to that of the selected-area electron diffraction pattern, though the degree of the equivalency between these patterns reduces at the high frequency region and the reproducibility of the intensity degrades when the number of images used in the image processing was decreased. By selecting areas in a reconstructed exit wave field, some electron diffraction patterns were obtained from the nano-areas without the influence of spherical aberration.