Embryonic stem cells (ESCs), due to their intrinsic capability to generate somatic cells of all three germ layers, are the potential sources of neural cells for cell replacement therapies. However, the empirical differentiation protocols and the lack of mechanistic understanding of the neural differentiation of ESCs has limited the utility of ESCs as a developmental model or as a cell source for neural cell population for replacement therapies. Coculturing ESCs with stromal cells is one of the extensively used methods to induce neural differentiation. Despite several studies attempting to identify neural inducing factors in stromal cell induced neural differentiation, self-regulatory effects of ESCs in the neural differentiation process remains unexplored. For the first time, we elucidate the self-regulatory role of mESCs on their neural cell differentiation by supplementing conditioned media from differentiating mESCs to the mESCs-PA6 cocultures and quantitatively evaluating the change in neural differentiation. Moreover, we use statistical tools to analyze the expressions of various growth and trophic factors and distinguish the factors produced primarily by PA6 cells versus mESCs in coculture. We observed that addition of the medium containing mESCs-secreted factors to the single mESCs colony cocultured with PA6 cells significantly enhanced the neural differentiation of mESCs compared to the medium extracted from the stromal cells only. Hierarchical clustering of gene expression data from PA6 and cocultured mESCs segregated two group of factors that are produced by the stromal cells and differentiating mESCs. Identifying the major soluble factors that drive and regulate the neural differentiation process in mESCs-PA6 coculture niche will help understand the molecular mechanisms of neural development. Moreover, it can be the first step toward developing novel protocols to differentiate stem cells with mESCs derived factors supplementation without using feeder cells with greater efficiency compared to existing approaches.