Achilles tendinopathy is common and treatment with eccentric exercises seems promising. We designed a prospective randomized clinical trial to test the hypothesis that eccentric calf muscle exercises reduce pain and improve function in patients with Achilles tendinopathy. Forty-four patients were recruited from primary care (mean age: 45 years; 23 women; 65% active in sports) and randomized to three treatment groups for 12 weeks: eccentric exercises, a night splint or a combination of both treatments. Pain and function were evaluated at 6, 12, 26 and 52 weeks by the Foot and Ankle Outcome Score. At 6 weeks, the eccentric group reported a significant pain reduction (27% compared with baseline, P = 0.007) which lasted for 1 year (42%, P = 0.001). The two groups treated with a night splint also reported significant but less pain reduction than the eccentric group. Differences between all the three groups were not significant. At 12 weeks, the eccentric group reported significantly less pain than the splint-only group (P = 0.04). More patients in the eccentric group than in the splint group returned to sport after 12 weeks. We conclude that eccentric exercises seem to reduce pain and improve function in patients with Achilles tendinopathy. Our results are in line with previous studies and strengthen the recommendation that patients should undergo an eccentric exercise program prior to considering other treatments such as surgery.