This article discusses the comparison of management at the Nihayatul Amal and Al-Muhajirin Islamic boarding schools, with the aim of knowing the similarities, differences, disadvantages and advantages between the two. Then this article is in the form of qualitative research with a critical analysis approach to the two Islamic boarding schools, and the data taken is the result of searching for previous research such as journals, books and so on as well as interviews with the alumni concerned. The result obtained is that these two Islamic boarding schools have their own characteristics, especially in terms of curriculum where the Nihayatul Amal boarding school is more inclined to the classical system but the Al-Muhajirin pesantren uses an integration system between classical and modern, as well as from the organization of the Al-Muhajirin pesantren they recruit service students who have been declared to have passed strata 1 while in the Nihayatul Amal boarding school only service students have participating in PKL activities, and from an institutional point of view, Nihayatul Amal has the status of a pure Islamic boarding school while Al-Muhajirin has the status of a foundation.