Skeletal muscle is one of the most abundant and dynamic tissues of the body, with a strong regenerative capacity. Muscle injuries can occur as a result of a variety of events, including tissue ischaemia. Lower limb ischaemia occurs when there is an insufficient nutrient and oxygen supply, often caused by stenosis of the arteries due to atherosclerosis. The aim of this study was to develop and validate a multiparametric scoring tool for assessing ischaemia severity in skeletal muscle in a commonly used pre-clinical animal model. Tissue ischaemia was surgically induced in mice by ligation and excision of the femoral artery. Calf muscles were carefully dissected, prepared for histological analysis and scored for inflammation, fibrosis, necrosis, adipocyte infiltration and muscle fibre degeneration/regeneration. Kendall’s coefficient of concordance (W) showed a very good agreement between the appraisers when scoring each individual histological feature: inflammation (W = 0.92 p-value 0.000), fibrosis (W = 0.94 p-value 0.000), necrosis (W = 0.77 p-value 0.000), adipocyte infiltration (W = 0.91 p-value 0.000) and fibre degeneration/regeneration (W = 0.86 p-value 0.000). Intra-rater agreement was also excellent (W = 0.94 or more, p-value 0.000). There was a statistically significant negative direct association between the level of muscle ischaemia damage and the calf muscle weight. Here, we have developed and validated a new multiparametric, semi-quantitative scoring system for assessing skeletal muscle damage due to ischaemia, with excellent inter- and intra-rater reproducibility. This scoring system can be used for assessing treatment efficacy in pre-clinical models of hindlimb ischaemia.