The aim of this study was to evaluate the effects of high intensity laser therapy (HILT) on tendon and ligament injury treatment in horses. Twenty six horses with tendinopathies were randomly assigned to a HILT treated or to a non-treated group. Each horse was subjected to the same rehabilitation programme. Horses from the treatment group underwent a series of fifteen HILT treatments with the same parameters. Clinical and ultrasound assessments were performed by the same veterinarian and were carried out before (day 0), during (day 13–15) and after treatment (day 38–40). Clinical evaluation included: pain, swelling and lameness of the affected limb. The ultrasound examination evaluated lesion echogenicity and lesion percentage. After the treatment, pain, swelling and lameness were significantly improved by HILT compared with the control group (p = 0.023, 0.008 and 0.044, respectively). No significant changes were found in lesion echogenicity degree between both groups in measurements taken during treatment (p = 0.188) and after treatment (p = 0.070). For lesion percentage reduction, the statistical modelling showed a significant improvement in the HILT group compared with the control group during (p = 0.038) and after treatment (p = 0.019). In conclusion, HILT promoted analgesic and anti-oedema effects, with visual lameness reduction in horses with tendon and ligament injuries, and reduced lesion percentage but did not influence change in lesion echogenicity.