A method and apparatus for generating a stereoscopic file defined based on a conventional International Standardization Organization (ISO) based media file format. The apparatus includes an encoder encoding first video data and second video data that are included in three-dimensional (3D) video data; and a file generating unit arranging the encoded first video data and second video data according to the information of a stereoscopic file format including boxes that are selected from boxes included in a conventional International Standardization Organization (ISO) based media file format in order to store and generate the stereoscopic file, and generating the stereoscopic file.