Musculoskeletal system impairment is a major cause of functional alterations in subjects with systemic sclerosis. Autologous hematopoietic stem cell therapy (AHSCT) may have an important role in the treatment functional of systemic sclerosis patients. The aim of this pilot study was to assess whether AHSCT interferes with the electromyographic activity of the masseter and temporalis muscles of subjects with systemic sclerosis. Before transplantation, seven subjects with systemic sclerosis (mean age [± SD], 40.1 ± 9.6 years) underwent electromyographic analysis of the masseter and temporalis muscles in mandibular tasks at rest, right and left laterality, protrusion and maximum voluntary contraction. Two months after AHSCT, the subjects re-evaluated using the same methods. Data were analyzed using the repeated-measure test, with p<0.05 considered to be statistically significant. Two months after AHSCT, there was reduction in normalized electromyographic activity in the dental clenching in maximal voluntary contraction, with significant differences, for the left temporal muscle (p=0.04). AHSCT in subjects with systemic sclerosis promotes alterations in stomatognathic system function, especially those related to electromyographic activity of masticatory muscles.