The purpose of this study is to improve the current Facility Management System of the Philippine National Railways, wherein, a combination of different knowledge with regards to the field of specialization of the researchers had taken place to resolve certain issues. The issues that were identified by the researchers are free loading passengers, passenger management, long queues and safety issues.  The researchers first acquire all the possible data that will be needed to assess the facility management and the totality of the system of PNR. After taking the different sets of data, statistical tools and other related literatures are used to get specific factors that will be considered to have a precise output. Finally, Industrial Engineering tools like quality function deployment (QFD), queuing theory, systematic layout planning (SLP) and systems and procedures were used for the design of the improved facility management system of the stations. These tools are intended for a specific issue. The common ground for the improvement of the three stations are the systems and procedures, that is why the researchers made a standard operating procedure/rule book for the employees that is in the perimeter of the station (i.e. security personnel, ticket booth personnel, mechanic and ticket inspectors). When in terms to the comparison of the present and improved facility management system of the Philippine National Railway, the researchers used Failure Mode and Effect Analysis (FMEA) to check whether the improved system will have a better effect for commuters when compared to the present system.