Abstract Background Denmark has inferior cancer survival rates compared with many European countries. The main reason for this is suggested to be late diagnosis at advanced cancer stages. Cancer diagnostic work-up begins in general practice in 85% of all cancer cases. Thus, general practitioners (GPs) play a key role in the diagnostic process. The latest Danish Cancer Plan included continuing medical education (CME) on early cancer diagnosis in general practice to improve early diagnosis. This dual aims of this protocol are, first, to describe the conceptualisation, operationalisation and implementation of the CME and, second, to describe the study design and outcomes chosen to evaluate the effects of the CME. Methods/Design The intervention is a CME in early cancer diagnosis targeting individual GPs. It was developed by a step-wise approach. Barriers for early cancer diagnosis at GP level were identified systematically and analysed using the behaviour system involving capability, opportunity and motivation described by Michie et al. The study will be designed as a geographical cluster randomised stepped wedge study. The study population counts 836 GPs from 417 general practices in the Central Denmark Region, geographically divided into eight clusters. GPs from each cluster will be invited to a CME meeting at a certain date three weeks apart. The primary outcomes will be primary care interval and GP referral rate on cancer suspicion. Data will be obtained from national registries, GP-completed forms on patients referred to cancer fast-track pathways and GP-completed online questionnaires before and after the intervention. Discussion To our knowledge, this will be the first study to measure the effect of a theory-based CME in early cancer diagnosis at three levels: GP knowledge and attitude, GP activity and patient outcomes. The achieved knowledge will contribute to the understanding of whether and how general practice’s ability to perform cancer diagnosis may be improved. Trial registration Registered as NCT02069470 on ClinicalTrials.gov.