Various types of natural hazards are inextricably linked to the process of underground hard coal mining. Ventilation hazards—methane and spontaneous combustion of coal—are the most dangerous; they pose a major threat to the safety of the workers and decrease the effectiveness of the whole coal production process. One of the methods designed to limit the consequences of such hazards is based on the selection of a ventilation system that will be suitable for the given mining area. The article presents a case study of an active longwall area, where—due to increasing ventilation hazard (methane and spontaneous combusting of coal)—the whole system was rebuilt. The U-type ventilation system was used in the initial stage of the extraction process, however, it often generated methane in amounts that exceeded the allowable values. Consequently, such conditions forced the change of the ventilation system from a U–type to Y–type system. The new system was installed during the ongoing mining process, unlike the usual practice. The article presents the results of tests on mine gas concentrations and descriptive statistics for both types of ventilation system. The results clearly demonstrate that the U-type longwall ventilation system, in the case of high methane release hazard, prevents safe and effective operation. At the same time, the use of this system limits the carbon oxidation reactions in the goaf, leading to spontaneous heating and combustion, which is confirmed by the low concentrations of gases—by-products of these reactions. In turn, the use of the Y-type longwall ventilation system ensures safe and effective operation in areas with high methane release hazard, but at the same time deteriorates the safety associated with the spontaneous combusting of coal. The presented case—both from a scientific and practical perspective—is quite interesting and greatly broadens the knowledge in the scope of an efficient ventilation system for underground workings.