For more than a decade Business-IT alignment (BITA) has been constantly ranked among the top-ten management issues for IT leaders. Many organizations value the advantages obtained when they are able to align their business and IT strategies. Although considerable models and frameworks have been developed to support organizations in their quest of achieving and sustaining BITA, still many of them face challenges because of some influential factors. While factors influencing BITA in organizations have been widely studied, the barriers in achieving BITA in the banking sector of a developing country remain largely unexplored. In this study we aim at exploring the factors that hinder BITA in the banking sector of a developing country. A case study research was conducted in four commercial banks in Burkina Faso with branches in more than ten other African countries. The data was collected through semi-structured interviews and also from internal documents and has been thematically analyzed. The main findings in this study shows that the delay in task execution, the lack of time to acquire new knowledge, the insufficiency of cross-sectional trainings, the dependency on telecom operators, the heavy workload of banking staff and the reluctance to hire more personnel considerably hinder BITA within the banks in Burkina Faso as a developing country. The results contribute to research in BITA and the limited knowledge about the factors hindering BITA in the banking sector of a developing country. Moreover the results of this research can help IT and business practitioners to further elaborate organizational skills training programs necessary for banks to improve their personnel's performance throughout their journey towards BITA.