Objective The purpose of this study was to describe the results of two treatment regimens for medial tibial stress syndrome (MTSS); a graded running programme and the same running programme with additional shockwave therapy (extracorporeal shockwave therapy; ESWT). Design A prospective observational controlled trial. Setting Two different sports medicine departments. Participants 42 athletes with MTSS were included. Intervention Patients from one hospital were treated with a graded running programme, while patients from the other hospital were treated with the same graded running programme and focused ESWT (five sessions in 9 weeks). Main Outcome Measures Time to full recovery (the endpoint was being able to run 18 min consecutively without pain at a fixed intensity). Results The time to full recovery was significantly faster in the ESWT group compared with the patients who only performed a graded running programme, respectively 59.7±25.8 and 91.6±43.0 days (p=0.008). Conclusions This prospective observational study showed that MTSS patients may benefit from ESWT in addition to a graded running programme. ESWT as an additional treatment warrants further investigation in a prospective controlled trial with the addition of randomisation and double blinding.