Exercise therapy is a key component in rehabilitation in both human and equine physiotherapy; however, in relation to the equine athlete only limited evidence is available for the use of exercises in rehabilitation. The aim of this review is to analyze studies that have evaluated trunk and hind limb muscle activation, and therefore provide an evidence base for the selection of exercises. Isolating activity to specific muscle groups or positioning to preferentially activate specific muscles is challenging for physiotherapists in horses; however, surface electromyography (EMG) data of muscular activity during locomotion could be applied to support selection of rehabilitation exercises used for this goal. The literature consistently reports the positive effect of increasing speed and slope on activity of longissimus dorsi, gluteus medius, tensor fascia latae, biceps femoris, vastus lateralis, and the abdominal muscles. However, there is still a lack of investigation into muscular activity during movements used for rehabilitation, despite exercises using training aids, poles and stretches being reported as therapeutic and strengthening. The use of EMG within the current studies does suggest that the relative patterns of muscle activity may be useful in comparing activity of one exercise with another and are worthy of further investigation in relation to rehabilitation exercise.