Cellular differentiation is accompanied by dynamic alterations in chromatin accessibility and lineage specific gene expression. One way in which chromatin structure is regulated is by the incorporation of histone variants such as H2A.Z. Essential for viability in higher eukaryotes, histone H2A.Z is incorporated into the nucleosome by two chromatin remodelling complexes p400 and SRCAP, the distinct functions of which remain uncharacterised. In numerous in vitro models of development, the dynamic and timely deposition of H2A.Z is key for efficient cellular differentiation. Although a highly robust and therapeutically relevant model of cellular development, the molecular mechanisms underpinning the differentiation of C3H/10T1/2 MSCs into thermogenic brown adipocytes remain poorly understood. This study aimed to establish both the localisation and function of H2A.Z during in vitro brown adipogenesis. During brown adipogenic lineage commitment, H2A.Z is dynamically redistributed to a number of stage specific promoters and enhancers, with this localisation associated with a parallel increase in expression of a subset of these genes. Whilst a partial reduction in H2A.Z expression had little effect on brown adipogenesis, reducing its incorporation into the nucleosome led to decreased brown adipogenic gene expression and diminished metabolic capabilities. Knockdown of essential SRCAP component p18Hamlet also led to a reduced H2A.Z accumulation at stage specific regulatory regions, suggesting a potential role for this remodelling complex in the deposition of H2A.Z.during lineage commitment. Together these observations suggest a role for H2A.Z in regulating gene expression during early brown adipogenesis.