Introduction: Making sure that best health services are provided, requires performance assessment in health sector. Assessment of efficiency is the first step in performance assessment. This research was aimed to assess of efficiency and comparison of its process in the Third Development plan and early years of the Fourth Development of all provinces in rural health sector. We attempt to determine the reference provinces, to find the sensitive indicators to provide solutions to increase the efficiency of each province.

Methods: This is an applied and descriptive survey research. Information about all provinces entered in Data Envelopment Analysis (DEA) model and analyzed. Data collecting tools were library and the internet documents. A questionnaire used to acquire the opinions of experts about the indicators.

Results: We found that Ardabil, Hamedan, Ilam, and Guilan provinces are no longer among the group of efficient provinces as in the Third Development Plan and Chaharmahal-O-Bakhtiari, Kurdistan, and Qazvin provinces joined the efficient provinces group in the Fourth Development plan. Some provinces were the most efficient provinces, but Sistan-O-Balouchestan, Kerman, Yazd, and Semnan have low efficiency in this area. Bed per population indicator and modern contraceptive prevalence rate indicator were determined as the most sensitive indicators.

Conclusion: In these two some provinces have the most efficient, and some others low efficiency in health sector. The efficiencies of the provinces compared, and reference provinces for each inefficient province distinguished. Modern contraceptive prevalence rate and available Bed per population indicators are selected as the most sensitive indicators.