Purpose Sickle cell disease (SCD) patients exhibit a limited exercise tolerance commonly attributed to anaemia, as well as hemorheological and cardio-respiratory abnormalities, but the functional status of skeletal muscle at exercise is unknown. Moreover, the effect of SCD genotype on exercise tolerance and skeletal muscle function has been poorly investigated. The aim of this study was to investigate skeletal muscle function and fatigue during a submaximal exercise in SCD patients. Methods Nineteen healthy individuals (AA), 28 patients with sickle cell anaemia (SS) and 18 with sickle cell-haemoglobin C disease (SC) performed repeated knee extensions exercise (FAT). Maximal isometric torque (Tmax) was measured before and after the FAT to quantify muscle fatigability. Electromyographic activity and oxygenation by near-infrared spectroscopy of the Vastus Lateralis were recorded. Results FAT caused a reduction in Tmax in SS (− 17.0 ± 12.1%, p < 0.001) and SC (− 21.5 ± 14.5%, p < 0.05) but not in AA (+ 0.58 ± 29.9%). Root-mean-squared value of EMG signal (RMS) decreased only in SS after FAT, while the median power frequency (MPF) was unchanged in all groups. Oxygenation kinetics were determined in SS and AA and were not different. Conclusion These results show skeletal muscle dysfunction during exercise in SCD patients, and suggest different fatigue aetiology between SS and SC. The changes in EMG signal and oxygenation kinetics during exercise suggest that the greater skeletal muscle fatigue occurring in SCD patients would be rather due to intramuscular alterations modifications than decreased tissue oxygenation. Moreover, SS patients exhibit greater muscle fatigability than SC.