Background: Excessive foot pronation is a causal mechanisms described in relation to injuries of the lower extremities. Evidence to support an effective treatment is insufficient. Objective: To investigate the effect of exercise and custom-made insoles to patients with excessive pronation and chronic pain conditions in the foot at short and long term follow-up. Methods: Single blinded Randomized Controlled Trial with 80 subjects randomized: (1) Standard Intervention, (2) Insole, (3) Exercise, and (4) Insole + Exercise. Exercise – 12 week supervised program. Insoles – individually molded and posted. Pain was measured during walking, resting and running. Static and dynamic foot postures were measured as calcaneal angle, navicular drift, drop and height. Results: The average duration of foot pain was 7.3 years. There was a significant pain reduction during walking within all groups at 4 and 12 months follow-up. No differences were seen between groups in any of the pain parameters. Weak correlations between changes in pain and foot postures were observed at baseline and one-year follow-up. Conclusion: A significant pain reduction was seen in all groups, none of the treatment modalities seem to be superior with the number of patients included. Compliance in the standard intervention group was a concern at 12 months.