We assessed the efficacy of cognitive behaviour therapy (CBT) delivered by general practitioners (GPs) to fatigued employees on sick leave. CBT had no substantial effect on clinical outcomes. In the present study, we aim to describe the treatment protocol and present an analysis of the delivery of the intervention. To assess protocol execution, GPs used standardized registration forms in each treatment session. A quality check was performed to assess whether CBT was completed according to protocol. Of the 71 patients starting CBT, 51 patients completed the intervention. There were no striking differences in protocol execution between those who recovered after CBT and those who did not recover. Although there were differences in the performance and delivery of CBT, there was no association between protocol execution and treatment results of individual GPs. Despite the lack of efficacy, the intervention received a positive evaluation from both patients and GPs. CBT completers who recovered did not receive a clearly different treatment than those who did not recover. In addition, successful GPs did not deliver a clearly different treatment than less successful GPs. The lack of efficacy can at least partly be attributed to the inadequacy of the intervention, whether it is the intervention itself or its delivery by GPs.