Leadership is trully important in the effort of increasing employees’ performance, as well as high spiritual intelligence which will motivate employees to do their jobs and responsibilities well and correctly, which is expected to be able to increase the performance of employees. Besides, necessity in paying attention to employees is also important. This study aims to analyse the role of working motivation as mediation of leadership and spiritual intelligence influence towards employees’ performance, which was done in the Regional Secretariat of Puncak Jaya Regency. 89 people involved in the present study. Technique employed in collecting the data was based on primer data, by giving questionnaires.by employing the analysis method of partially least square (PLS). It was found that affective leadership is not able to increase the employees’ performance. More effective leadership followed by high working motivation is able to increase the employees’ performance. As well as high spiritual intelligence, it is not able to increase the employees’ performance; on the other hand high spiritual intelligence followed by high working motivation is able to increase the employees’ performance. High working motivation is able to increase the employees’ performance. Therefore working motivation has role as full mediation towards leadership and spiritual intelligence influence towards employees’ performance in the Regency Secretariat of Puncak Jaya Regency.