Introduction As a natural phenomenon in the patient’s medication therapy, medication clinical complications potentially or concretely interrupt medical care consequential productivity for the patients. Medication related clinical complications include drug errors, drug side effects, drug interactions and drug usage-related challenges. The present research intends to explore the role that the Pharmacy Information System (PIS) may play in the management of medication complications with reference to the pharmaceutical societies of America and Australia in selected teaching, private and social services hospitals of the city of Isfahan. Methodology As an applied, descriptive-analytical study, this study has been conducted in teaching, private and social services hospitals situated in the city of Isfahan in 2011. The research population consisted of the PISs used in the hospitals under study. Research sample was the same as the population. The data collection instrument used was a self-designed checklist developed based on the guidelines of the American Society of Health System Pharmacists and Pharmaceutical Society of Australia validity of which was assessed by expert professors’ views. The data, collected by observation and interview methods, were put into SPSS 18 software to be analyzed. Findings The findings of the study revealed that among the 19 hospitals in question, the highest and lowest ranks in observing the societies of the pharmacists’ established standards related to medication therapy, i.e. registration of drug use status and drug interactions belonged to social services hospitals (mean score of %10.1) and private hospitals (mean score of %6.24), respectively. Conclusion Based on the findings, it can be claimed that the hospitals in question did not pay due attention to standards established by the societies of pharmacists regarding the medication therapy including register of drug usage status, drug interactions and drug side effects in their PISs. Hence, more thought must be given to the capabilities of the PIS in supporting the medication-related decisions and drug errors management so as to promote the treatment quality and satisfy medication therapy goals.