Widespread sex-dimorphism is observed in the mammalian immune system. Consistently, studies have reported sex differences in the transcriptome of immune cells at the bulk level, including neutrophils. Neutrophils are the most abundant cell type in human blood, and they are key components of the innate immune system as they form a first line of defense against pathogens. Neutrophils are produced in the bone marrow, and differentiation and maturation produce distinct neutrophil subpopulations. Thus, single-cell resolution studies are crucial to decipher the biological significance of neutrophil heterogeneity. However, since neutrophils are very RNA-poor, single-cell profiling of these cells has been technically challenging. Here, we generated a single-cell RNA-seq dataset of primary neutrophils from adult female and male mouse bone marrow. After stringent quality control, we found that previously characterized neutrophil subpopulations can be detected in both sexes. Additionally, we confirmed that canonical sex-linked markers are differentially expressed between female and male cells across neutrophil subpopulations. This dataset provides a groundwork for comparative studies on the lifelong transcriptional sexual dimorphism of neutrophils.