Background: Hospitals to improve the quality of health care and reduce the time and cost in providing health care should follow a strategic plan. Implementing strategies in hospitals is not possible easily and managers of hospitals face with barriers for implementing them. The aim of this study is to identify barriers to implementation of the strategic plan in the military and civilian hospitals.

Materials and Methods: This cross-sectional study was performed on senior managers, middle and executive in three military and three selected civilian hospitals of kerman in 2014. The total number of samples was 25 persons that had been selected as census. the instrument used, was a questionnaire that consists of two parts, the first part includes demographic specification and the second, consists of 4 areas, the human, process, structural, and institutional factors. Data was analyzed with SPSS 21.

Results: The results showed that barriers to implementation of the strategic plan in military and civilian hospitals is related to structural, human, processes and institutional factors respectively. There is no significant difference between the barriers to the implementation of the strategies in the military and civilian hospitals (P>0.05).

Conclusion: Structural factors, are the most important barrier in lack of strategies implementation in hospitals and managers should coordinates Structures with strategies in  medical centers under their management.