Higher education institutions are under increasing pressure to respond to societal needs which has in turn led to changes in the type of knowledge, competencies, and skills required from learners. Assessment of student learning outcomes is the most powerful educational tool for guiding effective learning. In Ethiopia, studies are scarce on assessment practices of learning outcomes of postgraduate students in biomedical and pharmaceutical sciences. This study investigated the assessment practices of learning outcomes of postgraduate students pursuing studies in biomedical and pharmaceutical sciences at the College of Health Sciences of Addis Ababa University. A quantitative cross-sectional study was conducted using structured questionnaires administered to postgraduate students and teaching faculty members in 13 MSc programs in biomedical and pharmaceutical sciences at the College of Health Sciences of Addis Ababa University. About 300 postgraduate and teaching faculty members were recruited with purposive sampling. The data collected included assessment methods, types of test items, and student preferences on assessment formats. Data were analyzed using quantitative approaches, descriptive statistics, and parametric tests. The study indicated that several assessment strategies and test items were practiced without a significant difference across fields of study. Regular attendance, oral questioning, quiz, group and individual assignments, seminar presentations, mid-term tests, and final written examination were commonly practiced assessment formats, while short question and long question essays were the most commonly used test items. However, students were not commonly assessed for skills and attitude. The students indicated they mostly preferred short essay questions, followed by practical-based examinations, long essay questions, and oral examination. The study identified several challenges to continuous assessment. Practice of assessing students' learning outcomes involves multiple methods focusing on assessing mainly knowledge; however, the assessment of skills appears inadequate, and several challenges appear to be hindering implementation of continuous assessment.