Abstract Background The rationale for the English National Chlamydia Screening Programme (NCSP) has been questioned. There has been little analysis, however, of what drove the NCSP’s establishment and how it was implemented. Such analysis will help inform the future development of the NCSP. This study used a qualitative, theory-driven approach to evaluate the rationale for the NCSP’s establishment and implementation. Methods Semi-structured interviews with 14 experts in chlamydia screening were undertaken. The interview data were analysed with policy documents and commentaries from peer-reviewed journals (published 1996–2010) using the Framework approach. Results Two themes drove the NCSP’s establishment and implementation. The first, chlamydia control, was prominently referenced in documents and interviews. The second theme concerned the potential for chlamydia screening to advance wider improvements in sexual health. In particular, screening was expected to promote sexual health services in primary care and encourage discussion of sexual health with young people. While this theme was only indirectly referenced in policy documents, it was cited by interviewees as a strong influence on implementation in the early years. However, by full rollout of the Programme, a focus on screening volume may have limited the NCSP’s capacity to improve broader aspects of sexual health. Conclusions A combination of explicit and implicit drivers underpinned the Programme’s establishment. This combination may explain why there was widespread support for its introduction and why implementation of the NCSP was inconsistent. The potential to improve young people’s sexual health more comprehensively should be made explicit in future planning of the NCSP.