Key points Loss of skeletal muscle capillaries is thought to contribute to a reduction in exercise tolerance, but the relative contribution of a compromised microcirculation with disease, in isolation of co‐morbidities, to impaired muscle function is unknown.We therefore developed a novel method to randomly occlude capillaries in the rat hindlimb to mimic the capillary rarefaction observed in many conditions.We demonstrate that muscle fatigue resistance is closely coupled with functional microvascular density, independent of arterial blood flow, while disturbance of the microcirculation leads to long‐term impairment of muscle function if left untreated.Mechanical stretch due to muscle overload causes a restoration of fatigue resistance via angiogenic remodelling.These observations highlight the importance of a healthy microcirculation and suggest that restoring impaired microvascular supply, regardless of disease co‐morbidities, will assist recovery of exercise tolerance in a variety of conditions that limit quality of life. To what extent microvascular rarefaction contributes to impaired skeletal muscle function remains unknown. Our understanding of whether pathological changes in the microcirculation can be reversed remains limited by a lack of basic physiological data in otherwise healthy tissue. The principal objectives here were to: (1) quantify the effect of random microvascular rarefaction on limb perfusion and muscle performance, and (2) determine if these changes could be reversed. We developed a novel protocol in rats whereby microspheres injected into the femoral artery allowed a unilateral reduction in functional capillary density in the extensor digitorum longus (EDL), and assessed acute and chronic effects on muscle function. Simultaneous bilateral EDL force and hindlimb blood flow measurements were made during electrical stimulation. Following functional capillary rarefaction there was an acute microsphere dose‐dependent reduction in muscle fatigue resistance (P < 0.001), despite preserved femoral artery perfusion. Histological analysis of EDL samples taken from injected animals confirmed a positive correlation between the proportion of functional capillaries and fatigue resistance (P = 0.002). Such impaired performance persisted for at least 2 weeks (P = 0.016). Concomitant mechanical overload improved both perfused capillary density and fatigue resistance (P<0.05), confirming that the capacity for muscle remodelling was retained following chronic distributed ischaemia, and that the impact of capillary rarefaction could be alleviated. These results demonstrate that loss of functional capillaries is detrimental to muscle function, even in otherwise healthy tissue, independent of arterial perfusion. Restoration of muscle performance following a mechanical overload stimulus indicates that angiogenic treatments to alleviate microvascular rarefaction may be key to restoring exercise tolerance.