AJABS is an internationally refereed journal published jointly by the International Network on Animal and Biomedical Science and Technology for Africa (INABSTA), an initiative of the NEPAD Council Education Commission (NCEC), Makerere University (College of Veterinary Medicine, Animal Resource and Bio-Security - CoVAB) and Uganda Veterinary Association.

The mandate of Makerere University Journal of Agricultural and Environmental Sciences (MUJAES) is to disseminate research finds in key areas covering agricultural, food, forestry, and environmental sciences. MUJAES publishes 2 issues per year. Papers are available online, with occasional prints. 

The Uganda Journal of Education (UJE) is a peer-reviewed journal hosted by the College of Education and External Studies, Institute of Education Research Makerere University. It seeks critical reviews and in-depth analyses or study findings in all areas of education.  UJE serves as a communication medium among education professionals, policy makers, researchers, students and the community. UJE encourages the dissemination of studies aimed at identifying problems, informing policy and contributing towards reform and the general development of education in the country and region. 

Mawazo (sing. wazo) is a comprehensive Kiswahili word covering the following activities of the mind: meditations, reflections, thoughts, opinions, and ideas. Mawazo is a multidisciplinary international, peer reviewed journal published in English by the College of Humanities and Social Sciences, Makerere University. It is a scholarly journal of research and opinions in the Humanities and Social Sciences. Mawazo was first published in June 1967 as a publication of the Faculties of Arts and Social Sciences, Makerere University to promote national consciousness and pan-Africanism through the promotion of basic research in the humanities and social sciences. Mawazo seeks to disseminate cutting-edge research and opinions relevant and reflective of African realities. The thorough multidisciplinary character of the journal enables it to analyse the African conditions in a more holistic manner.

The Makerere Historical Journal publishes peer-reviewed articles, reports and book reviews on topics related to Ugandan and eastern African history, archaeology and heritage. Originally established in 1975, the Journal is the publication of the Department of History, Archaeology and Heritage Studies at Makerere University. It publishes original research articles, reports on sources and events, and book reviews especially of books published within Uganda. 

African Health Sciences is an internationally refereed journal publishing original articles on research, clinical practice, public health policy, planning, implementation and evaluation, in the health and related sciences relevant to Africa and the tropics. From 2005 African Health Sciences will be published four times a year in March, June, September and December. 

The One Health and Global Health Security Journal is an international journal on infectious diseases hosted by Makerere University Press that covers emerging and re-emerging public health aspects at human-animal-environment interface, as well as biomedical research with particular emphasis on topics relevant to human, animal and ecosystems health.

IJADE provides an international forum for research in the field of the art and creative education.

The "African Journal of Leadership and Conflict Management" focuses on the study of leadership and conflict resolution within the African context. It explores how leadership styles, particularly transformational leadership, influence conflict management strategies and outcomes in various institutions, including educational ones. The journal also examines the role of democratic capacity building, community engagement, and indigenous knowledge in achieving reconciliation and stability in post-conflict societies. 

The East African Journal for Peace and Human Rights (EAJPHR) is an international, peer-reviewed, bi-annual scholarly publication of the Human Rights and Peace Centre (HURIPEC) at the School of Law, Makerere University. The Journal has since its inception in 1993 remained at the forefront of igniting intellectual and policy debates on contemporary governance and human rights issues in the East African region and beyond. It seeks to provide a platform to scholars, researchers and practitioners in the fields of governance and human rights to disseminate cutting-edge research and share knowledge and experiences.