Payroll accounting system is a series of calculation procedure and payment of salary as a whole for employees efficiently and effectively. The purpose of this research is to know how the employee payroll accounting system applied and flow chart with evaluation in the payroll accounting system in Public Works and Spatial Planning of Cirebon District. This research used descriptive qualitative, because this research aims to describe the application of payroll accounting system. The result of this research proves that the application of payroll accounting system in Public Works and Spatial Planning of Cirebon District consist of interrelated elements, there are document, related functions, procedures that form the payroll system and accounting recording. This research also proves that Public Works and Spatial Planning of Cirebon District had internal control in monitoring process of payroll accounting system