BACKGROUND: The current drive to strengthen health systems provides an opportunity to develop new strategies that will enable countries to achieve targets for millennium development goals. In this paper, we present a proposed framework for evaluating a new health system strengthening intervention in Zambia known as Better Health Outcomes through Mentoring and Assessment. APPROACH: We briefly describe the intervention design and focus on the proposed evaluation approach through the lens of systems thinking. DISCUSSION: In this paper, we present a proposed framework to evaluate a complex health system intervention applying systems thinking concepts. We hope that lessons learnt from this process will help to adapt the intervention and limit unintended negative consequences while promoting positive effects. Emphasis will be paid to interaction and interdependence between health system building blocks, context and the community.