The purpose of this study is to show the problems and to suggest improvement methods on the introduction of Pharmacy Information Systems(PIS) after medical reform. Medical reform have influenced many aspects of patients, doctors and pharmacists. In the case of pharmacy, information systems have been key role in the pharmacy management after medical reform. Although one year has been passed, there are still many problems. The size of system development company, A/S, the ability of programmer and the frequent change of related laws and ordinances cause difficulties in the operation of PIS. In this paper, the case of A pharmacy in daegu was investigated for the operation of PIS. Analytic Hierarchy Process(AHP) and mathematical programming methods can be used for reducing the aspect of subjectivity and considering the resource constraints.