He was awarded his bachelor of Medicine and bachelor of General Surgery degree of Makerere University in 1981, MSc degree in International Health in 1986, School of Tropical Medicine, The University of Liverpool, UK and infectious diseases at Case Western Reserve University School of Medicine, USA in1989. He is a Chest Physician and Public Health Specialist currently working as a Honorary Lecturer, Department of Internal Medicine, School of Medicine, Makerere University College of Health Sciences and Head of TB Unit, Mulago Hospital, the largest University teaching and national referral hospital in Uganda. Alphonse has a wealth of experience and a rich background of research in TB chemotherapy clinical trials, TB diagnostics, epidemiology and operational research and HIVTB interactions. He has published well over 74 articles as author and co-author in peer reviewed journals in the last 20 years.
He has been Principal and co- investigator in many studies including the following studies sponsored by: NIH/DAIDS, NIH/TBRU, NIH/CDC, CDC, WHO, CDC/TB Trials Consortium, Doris Duke, Welcome Trust among others. Dr. Okwera is the site Principal Investigator in Uganda, PanACEA TB Project as well as an investigator, TBRU Project, Kampala.