A method of manufacturing a honeycomb structure having a plugged portion, which is faster and cheaper to manufacture, and a manufacturing apparatus thereof. A film is attached to an end face of a honeycomb structure in a state where the honeycomb structure is positioned in a table portion having a through hole into which the end face portion of the honeycomb structure is to be inserted, and the film is held in a flat state where a remaining portion of the film which is not attached to the end face is attached to the table portion. Then, holes opened so as to correspond to the openings of a part of cells are formed in the film to form the film as a mask, and a plugging material having fluidity is supplied onto the mask or onto the same plane as the mask to fill the cells with the plugging material.