Melanocyte development involves key pathways that are often recapitulated during melanoma initiation, highlighting the importance of understanding the regulators that control these early processes and also contribute to cancer onset. Our study identifies mgat4b , a glycosyl transferase involved in selective N -glycan branching enriched in pigment progenitors, as a key regulator of directional melanocyte migration and establishment of melanocyte stem cell (McSC) pool during early development. Single cell RNA (scRNA) sequencing analysis in zebrafish upon targeted disruption of mgat4b reveals, that migratory melanocyte progenitors marked by galectin expression fail to persist. Lectin affinity proteomic analysis reveals the glycosylation of key melanocyte proteins GPNMB, KIT, and TYRP1 to be under the control of MGAT4B in melanocytic cells. Additionally, mislocalization of Junctional plakoglobin (JUP) explains the observed defects in cell adhesion and migration to be regulated by MGAT4B but not its isozyme MGAT4A. Our meta-analysis further reveals that melanoma patients with both the BRAF V600E mutation and elevated MGAT4B levels have significantly worse survival outcomes compared to those with only the BRAF V600E mutation. By leveraging the MAZERATI platform to model BRAF V600E driver mutation in vivo , we show that mgat4b mutant cells fail to aggregate and initiate tumors. RNA profiling of the transformed melanocytes revealed cell-cell junction, adhesion and ECM binding to be probable contributing factors that resulted in the failure of tumor onset. Using a small-molecule inhibitor we demonstrate the inhibitory role of this complex N -glycosylation in the progression of early-stage melanoma. Our study underscores the importance of selective N -glycan branching in both melanocyte development and melanoma initiation, suggesting MGAT4B as a promising therapeutic target for melanoma treatment.