Sertoli cells, the only somatic cells within seminiferous tubules, associate intimately with developing germ cells. They not only provide physical and nutritional support but also secrete factors essential to the complex developmental processes of germ cell proliferation and differentiation. The Sertoli cell transcriptome must therefore adapt rapidly during the different stages of spermatogenesis. We report comprehensive genome-wide expression profiles of pure populations of Sertoli cells isolated at five distinct stages of the first wave of mouse spermatogenesis, using RNA sequencing technology. We were able to reconstruct about 13’901 high-confidence, non-redundant coding and non-coding transcripts, characterized by complex alternative splicing patterns with more than 45% comprising novel isoforms of known genes. Interestingly, roughly one fifth (2’939) of these genes exhibited a dynamic expression profile reflecting the evolving role of SCs during the progression of spermatogenesis, with stage-specific expression of genes involved in biological processes such as cell cycle regulation, metabolism and energy production, retinoic acid synthesis and blood testis barrier biogenesis. Finally, regulatory network analysis identified the transcription factors Endothelial PAS domain-containing protein 1 (EPAS1/ Hif2α), Aryl Hydrocarbon Receptor Nuclear Translocator (ARNT/Hif1β) and Signal Transducer and Activator of Transcription 1 (STAT1) as potential master regulators driving the Sertoli cell transcriptional program. Our results highlight the plastic transcriptional landscape of Sertoli cells during the progression of spermatogenesis and provide valuable resources to better understand SC function and spermatogenesis and its related disorders such as male infertility.