Paternal histone modifications are extensively remodeled during mammalian spermatogenesis. This remodeling is significant because histone modifications encode gene regulatory information important for fertility and potentially for development in the next generation. Most insight into these epigenetic changes has been gleaned from chromatin immunoprecipitation (ChIP)-seq analysis of male germ cells during the meiotic and postmeiotic stages of spermatogenesis due to their abundance in seminiferous tubules and long-standing methods for their purification. However, there is a paucity of research defining the epigenetic landscape of earlier spermatogenic populations, including spermatogonia, mainly because cell yields are low after purification, resulting in suboptimal conditions for ChIP-seq experiments. The recent emergence of Cleavage Under Targets and Tagmentation (CUT&Tag) as a tool to profile genome-wide histone modifications in low numbers of cells offers promising opportunities to overcome the limitations of ChIP-seq analysis in spermatogonia. Here, we describe a protocol that combines fluorescence-activated cell sorting with an optimized CUT&Tag workflow for as few as 50,000 dissociated, sorted cells to generate high-quality and reproducible datasets that faithfully capture enrichment of histone modifications in differentiating spermatogonia. This protocol will enable researchers to investigate the epigenetics of premeiotic cells in the male germ line easily and robustly.