Histopathology and cytopathology are crucial in the diagnosis and control of disease, particularly in Sub-Saharan Africa (SSA) where infectious as well as non-communicable diseases are rampant. While histopathology and cytopathology are vital, there is sparse literature documenting the most prevalent methods applied in SSA. We aim to establish the most recently widely applied diagnostic methods in SSA histopathology and cytopathology services. A systematic review facilitated by the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines will be conducted by searching English literature databases between 2000 and 2024. Eligibility screening of studies, data extraction, and appraisal via standardized instruments will be conducted. This review aims to synthesize the best available evidence for histopathology and cytopathology practice in SSA, identify strengths and limitations, and identify areas of improvement. The findings will inform the creation of context-matched guidelines and training for medical laboratory scientists and improve diagnostic capacity in SSA.