Amniotic fluid stem cells (AFSc) are a very heterogeneous subtype of stem cells with a broad multi potential. They could be used to treat congenital malformations or diseases. Recently, mesoangioblasts, resident pericytes of skeletal muscles, were shown to undergo muscle differentiation in vitro and in vivo. In this study we focused on the identification of an AFS subtype with pericytic characteristics and evaluate its myogenic potential. We identified monoclonal AFSc lines expressing alkaline phosphatase activity (ALP) and the canonical pericytic markers neural-glial-2 chondroitin sulphate proteglycan (NG2), platelet derived growth factor receptor α and β (PDGFR-α, -β) and α smooth muscle actin (α-SMA). These cells were able to integrate into the newly formed myotubes when co-cultured with the C2C12 cells. To test the paracrine effects of these AFSC on muscle regeneration, we assessed their affects in a transwell assay with acutely injured myotubes. AFSc were able to modulate the expression of specific growth factors involved in muscle regeneration, such as Transforming Growth Factor β (Tgfβ), Interferon γ (Ifnγ), Hepatocyte Growth Factor (Hgf) and Matrix Metalloproteinase 2 (Mmp2). When AFSc were injected in injured muscles they ameliorated muscle repair as measured by the reduction of centronucleated fibers and fibrosis. Interestingly, the transcriptional program of growth factor response in vitro is observed in large part in the in vivo xenograft experimental model, with the extension of Myostatin and Matrix Metalloproteinase 9 (Mmp9). Our data suggest that AFSc subtype with pericytic characteristics have the ability to modulate muscle regeneration in vitro and in vivo.