The purpose of the present invention is to provide: a packaging container that can be industrially mass-produced, that can be used as Modified Atmosphere Packaging (MAP) while ensuring sealing performance, and that allows contents to be displayed in a three-dimensional manner; a packaged product contained in the packaging container; and a manufacturing method and manufacturing apparatus for the packaging container. This packaging container has: a container main body having a bottom face part and sidewall parts, and having a flange at the upper end part periphery of the sidewall parts; and a lid material heat-sealed to the flange. The lid material is made of a film or sheet. A pair of opposing sidewall parts has the same shape, and upper end parts of the pair of side wall parts are at least positioned higher than the upper end parts of another pair of opposing sidewall parts.