Aim of the study is to find the perceptions of Presbyterian Church leaders about HIV prevention in Aizawl, Mizoram. For the study, mixed method was followed for data collection. From 15 Presbyterian churches, 293 Church leaders representing four groups, that is, Pastor/Elder, Women, Youth and Men were randomly selected and used self-administered questionnaire for the purpose of understanding perceptions on HIV prevention from them. Chi-square test was done to understand the associations with different factors. Qualitative information was collected using in-depth interviews from 12 and focus group discussions from 3 leaders. Thirty four percent of leaders expressed willingness to advocate condom for prevention. Majority (97.3 %) of leaders felt they need to intervene and 90% were for including HIV prevention in church services. Two third (70 %) felt Biblical disobedience causes HIV and 80% felt homosexuals deserved it. Leaders preferred abstinence, marital fidelity, and condom use as appropriate methods for HIV prevention. About 70% agreed with the Church statement, ‘condoms encourage pre-marital sex’, and above 80% reported condom prevents HIV. Analysis show, contacting person living with HIV (PLHIV) was not positively associated with willingness to advocate condom use. Church leaders their inability quoting the church doctrine as constraint. Many felt disobedience to Biblical teachings and sinful acts result in HIV. Leaders felt, educating church leaders and disseminating sex education using church media were effective methods for HIV prevention.