The objective of this study is investigating effective factors on users’ resistance to apply Accrual Accounting System (AAS) at Iranian Medical Science Universities. This study is a field-survey research. Subjectives of this research include financial managers of Medical Science Universities and Health Centers in Iran in 2017. According to research hypothesis and variables the researcher has made a questionnaire using Morgan & Krejcie sampling table, 323 questionnaires were filled by the subjects. SPSS and LISREL and Structural Equal Model (SEM) have been used to data analysis. Financial managers of Medical Science Universities and Health Centers, believe that there are five factors in applying or using Accrual Accounting System (AAS), affecting users’ resistance. These factors include: top manager’s idea, colleques’ viewpoint, personals’ ability, adequaty of information system, and external beneficiary’s viewpoint. The results show that majority of research subjects are among professional personnel who have enough information about accounting system of medical science universities. Therefore, accounting to research findings, almost 96 percent of subjects believe that the effective factors on user’ resistance to the implementation Accrual Accounting System (AAS) in medical science universities have significant effect.