Based on the World Health Organization's health systems strengthening framework, the Health Systems Governance and Accountability (HSGA) intervention to strengthen public health leadership/management, service integration and outcomes was developed in the Free State. This study describes the process to implement and measure the effects of the HSGA intervention for system-wide improvement of leadership/management under routine conditions in a resource-constrained setting. Based on normalisation process theory, participatory discussions were held with health managers, staff and local stakeholders to attain buy-in. Evaluation of the implementation process considered progress in improving leadership/management through application of the Balanced Scorecard (BSC). All provincial reporting units were assessed during 2014/15 and again during 2015/16. The mean scores on three BSC perspectives improved statistically significantly from 2014/15 to 2015/16: customer (p=0.0085), internal business processes (p=0.0008) and finance (p=0.0001). Overall leadership/management also improved significantly (p=0.0007). Improvement in leadership/management resulting from implementation of the HSGA intervention was observed during the two years under study. From this experience, successful implementation of a health systems strengthening intervention hinges on a participatory design, appropriate use of theory, as well as application of an evaluation approach to assess the success of implementation.