Precise developmental staging of embryos is critical for experimental methods that compare different groups of embryos in developmental biology. During development, gene and protein expression levels change dynamically as cells acquire sequentially more restricted cell fates, from pluri- or multipotent cells to germ layers and to differentiated cells. In particular, zebrafish embryos experience rapid transcriptional changes at the mid-blastula transition, when zygotic transcription is activated in specific domains along the dorsoventral and anteroposterior axes and maternal transcripts are degraded. During these rapid and widespread transcriptional changes, precise staging is needed to accurately compare one group of experimental embryos to another that differ in some experimental variable, such as mutant versus wild-type embryos, or embryos receiving two different experimental treatments. Precise staging ensures that an observed change in gene or protein expression between the experimental groups is due to the experimental variable and not to a difference in developmental stage caused by asynchrony in early development. However, zebrafish embryos exhibit rapid cell divisions and subtle morphological changes during the mid-blastula period, making it difficult to accurately stage embryos using morphology or timing alone. Here, we present a method to quantitatively stage zebrafish embryos based on cell count during the mid-blastula period. Our method can be applied to any zebrafish experiment performed during the mid-blastula period, by counting nuclei in sibling embryos of the experimental ones. After staining with a nuclear marker, nuclei are imaged with a confocal microscope and then quickly identified and counted with standard imaging software. Overall, this quantitative staging method can increase experimental rigor and decrease variability in experiments during the mid-blastula period.