The purpose of this study was to analyze the effect of the application of a safety management system (SMS) and safety culture with safety motivation as a mediating variable on flight safety performance. The population in this study were all AirNav Indonesia ATC personnel at the JATSC Branch Office (Jakarta Air Traffic Service Center) totaling 381 people. Sampling by simple random sampling method with a total of 160 people. Data processing was carried out using SPSS and Amos software using a structural equation model (SEM) technique. The results showed that of the 5 direct influence hypotheses tested, there was one that was not significant, namely the Effect of the SMS that did not affect flight safety performance at AirNav Indonesia. The highest coefficient of influence that determines flight safety performance at AirNav Indonesia is safety motivation. This means that the higher the Safety Motivation that occurs in this agency, it will greatly affect the level of performance at AirNav Indonesia. Therefore, it is the leadership's task to keep the safety motivation that occurs among AirNav Indonesia is not a problem, so that flight performance is maintained and remains good. The role of the safety motivation variable can act as a mediator on the effect of implementing a SMS on flight safety performance through safety motivation at AirNav Indonesia. This means that the higher the Safety Motivation that occurs in this agency, it will greatly affect the level of performance at AirNav Indonesia. Therefore, it is the leadership's task to keep the safety motivation that occurs among AirNav Indonesia is not a problem, so that flight performance is maintained and remains good. The role of the safety motivation variable can act as a mediator on the effect of implementing a SMS on flight safety performance through safety motivation at AirNav Indonesia. This means that the higher the Safety Motivation that occurs in this agency, it will greatly affect the level of performance at AirNav Indonesia. Therefore, it is the leadership's task to keep the safety motivation that occurs among AirNav Indonesia is not a problem, so that flight performance is maintained and remains good. The role of the safety motivation variable can act as a mediator on the effect of implementing a SMS on flight safety performance through safety motivation at AirNav Indonesia.