Brachyury is a key transcription factor, which is required for mesoderm lineage development. Here, we have generated a Brachyury/TBXT-2A-EGFP knock-in Reporter line in the BJNhem20 human embryonic stem cell line, using CRISPR/Cas9-based gene editing. Successful gene editing was verified by DNA sequencing and comparing endogenous gene expression to reporter gene expression. This reporter line represents an important tool for tracking and assessing mesoderm differentiation.