Background: The education and activation programme (EAP) aims at coping with psychosocial determinants to prevent the development of chronic shoulder complaints (SCs). The effect of the EAP on functional limitations and patient-perceived recovery after 6 and 26 weeks is evaluated in a randomised clinical trial. Methods: Patients with SCs present at rest or elicited by movement and lasting no longer than 3 months were allocated at random to either EAP as an addition to usual care (UC), or to UC only. Measurements were taken at baseline and after 6 and 26 weeks and were analysed by means of multilevel analysis for the group effect. EAP was administered by GPs or by an ambulant therapist (CDB). Patients in the UC group were given UC by their own GP. Results: Multilevel analysis failed to show a significant effect of the EAP on either functional limitations or patient-perceived recovery. Analysis showed coincidentally a relation between catastrophising at baseline and functional limitations. Conclusion: The EAP has no significant effect on the outcome of SCs after 6 and 26 weeks. The relation between catastrophising at baseline and functional limitations suggests that an intervention focusing specifically on catastrophising may be more successful in reducing functional limitations in the long term. Further research is however needed to evaluate the effect of catastrophising at baseline on the course of SCs. Trial registration: Current Controlled Trials ISRCTN71777817.