The therapeutic strategies for neurodegenerative diseases still represent a vast research field because of the lack of targeted, effective and resolutive treatment for neurodegenerative diseases. The use of stem cell-based therapy is an alternative approach that could lead to the replacement of damaged neuronal tissue. For this purpose, adult mesenchymal stem cells (MSC), including periodontal ligament stem cells (PDLSCs), could be very useful for their differentiation capacity, easy isolation and the ability to perform an autologous implant. The aim of this work was to test whether the Moringin [4-(α-L-rhamnosyloxy) benzyl isothiocyanate; GMG-ITC], an isothiocyanate extracted from Moringa oleifera seeds, was able to induce PDLSCs toward neural progenitor differentiation. Next-generation transcriptomics sequencing showed that moringin treatment increased the expression of genes involved in neuron cortical development and in particular in neuron belonging to upper and deep cortical layers. Moreover, moringin treatment upregulated genes involved in osteogenesis and adipogenesis although with a lower fold change compared to upregulated genes involved in neuronal differentiation. Finally, moringin did not induce the expression of oncogenes resulting in a safe treatment.