By applying an one-dimensional aeronomic model of the upper atmosphere of the close-in giant planet HD 209458b, we study the reaction of the planetary atmosphere to an additional heating caused by the influence of a stellar flare. It is shown that the absorption of additional energy of the stellar flare in the extreme ultraviolet leads to local atmospheric heating, accompanied by formation of two shock waves, propagating in the atmosphere. We discuss possible observational manifestations of the shocks and feasibility of their detection.