This research aims to compare merit system implementation for top leaders filling positions in North Buton Regency and Kendari City. Another objective is determining the driving and inhibiting factors for implementing the merit system in the two regional government agencies. This study employs the merit principle theory (Stahl, 1979) and the best person theory (McCourt, 2007). The method used is descriptive qualitative; the primary data are obtained from interviews, and secondary data are obtained from documentation and archives. The informant selection technique uses a purposive technique. The research results show that in top leaders filling positions, there are significant differences between the North Buton Regency and Kendari City regarding the merit system principles. The factors influencing the implementation of merit systems in both areas are socio-cultural, political, and organizational. The driving factors to enforce the merit system in Kendari City are greater than its inhibiting factors, while North Buton Regency is the opposite. Nearly all the driving factors in Kendari City are the inhibiting factors in North Buton Regency. However, there is a similarity of non-discriminatory treatment in both local governments. This research contributes to the knowledge and literature pertaining to top leader selection practices in developing countries.