IntroductionThe ‘learning healthcare system’ (LHS) has been proposed to deliver better outcomes for patients and communities by analysing routinely captured health information and feeding back results to clinical staff. This approach is being piloted in the Connected Health Cities (CHC) programme in four regions in the north of England. This article describes the protocol of the evaluation of this programme.Methods and analysisIn designing this evaluation, we had to take a pragmatic approach to ensure the feasibility of completing the work within 1 year. Furthermore, we have designed the evaluation in such a way as to be able to capture differences in how each of the CHC regions uses a variety of methods to create their own LHS. A mixed methods approach has been adopted for this evaluation due the scale and complexities of the pilot study. A documentary review will identify how CHC pilot study deliverables were operationalised. To gain a broad understanding of CHC staff experiences, an online survey will be offered to all staff to complete. Semi-structured interviews with key programme staff will be used to gain a deeper understanding of key achievements, as well as how challenges have been overcome or managed. Our data analysis will triangulate the documentary review, survey and interview data. A thematic analysis using our logic model as a framework will also be used to assess progress against the CHC programme deliverables and to identify recommendations to support future programme decision-making.Ethics and disseminationEthical approval was granted by The University of Manchester Ethics Committee on 24 May 2018. The results will be actively disseminated through peer-reviewed journals, conference presentations, social media, the internet and various stakeholder/patient and public engagement activities.