BACKGROUND: The importance of health policy and systems research and analysis (HPSR+A) has been increasingly recognised, but it is still unclear how most effectively to strengthen the capacity of the different organisations involved in this field. Universities are particularly crucial but the expansive literature on capacity development has little to offer the unique needs of HPSR+A activity within universities, and often overlooks the pivotal contribution of capacity assessments to capacity strengthening. METHODS: The Consortium for Health Policy and Systems Analysis in Africa 2011-2015 designed and implemented a new framework for capacity assessment for HPSR+A within universities. The methodology is reported in detail. RESULTS: Our reflections on developing and conducting the assessment generated four lessons for colleagues in the field. Notably, there are currently no published capacity assessment methodologies for HPSR+A that focus solely on universities - we report a first for the field to initiate the dialogue and exchange of experiences with others. Second, in HPSR+A, the unit of assessment can be a challenge, because HPSR+A groups within universities tend to overlap between academic departments and are embedded in different networks. Third, capacity assessment experience can itself be capacity strengthening, even when taking into account that doing such assessments require capacity. CONCLUSIONS: From our experience, we propose that future systematic assessments of HPSR+A capacity need to focus on both capacity assets and needs and assess capacity at individual, organisational, and systems levels, whilst taking into account the networked nature of HPSR+A activity. A genuine partnership process between evaluators and those participating in an assessment can improve the quality of assessment and uptake of results in capacity strengthening.