The impacts of changing climate on agriculture have consequences on livelihoods and food security. Smallholder farmers, who have heterogeneous farming systems and limited resources, compounded with multiple risks, are greatly affected. There has been limited research showing how vulnerability assessments have evolved in the smallholder agricultural sector of Africa overtime. This study systematically reviewed recent publications on vulnerability studies, especially among smallholder agricultural systems, to provide an overview of current developments in theory and practice of vulnerability in Africa over the last decade. The findings indicate an increase in vulnerability assessments undertaken across Sub Saharan Africa. Despite progress made in the application of enhanced conceptual frameworks and methods, at least four important gaps exist in the assessment process namely, inadequate engagement of local perspectives and knowledge, lack of clarity in the operationalisation of vulnerability, lack of comprehensiveness of measurement criteria employed and relevance of assessment in decision support. Notwithstanding these challenges, there exist opportunities to geographically improve assessments across Africa. In order to produce knowledge to traverse projected changes in climate systems for agricultural economies and to ensure sustainable smallholder livelihoods, we suggest that future research efforts should be oriented towards providing more information to enlighten science, policy and practice for informed decision-making and evidenced based policies. This requires evaluation of adaptation capacity as a critical aspect of vulnerability assessment to provide guidance and inform effective decision-making on allocation of scarce resources (prioritization); understand trade-offs management and implementation to build understanding among stakeholders that guide possible pathways to reduce vulnerability.