The pharyngeal foregut endoderm (PFE) gives rise to several important organs including the thyroid, thymus and parathyroid glands. In mice and humans, defects in the development of PFE can lead to thymic aplasia and aberrations in thymic epithelial cell (TEC) function can lead to immunodeficiency or autoimmune disease. Successful differentiation of pluripotent stem cells (PSCs) to PFE could provide a renewable cell source that enables the study of human diseases that originate in the PFE. Here, I identify signaling pathways that influence the differentiation of PSCs to PFE. Firstly, using a novel mouse reporter PSC line we develop a protocol that generates a Pax9 expressing population that is enriched for PFE markers and upon transplantation can form organized epithelial structures. However, since this protocol was inefficient for human PSCs, we subsequently identified additional signaling pathways required for the efficient generation of human PFE and determined a key role for retinoic acid. Upon transplantation, the human PFE gives rise to TECs, a ventral PFE derivative. Finally, to facilitate future investigation into the gene regulatory networks in PFE, we develop a CRISPR-effector system to modulate endogenous gene expression in PSCs. We demonstrate that developmentally relevant genes can be repressed or induced, thereby influencing the cellular state. These data present strategies to generate cells of the PFE lineage from PSCs, facilitating the production of cells for patient-specific disease modeling or cell replacement therapies, and a method to interrogate gene and regulatory element function in PFE and its derivatives.