Early pregnancy loss has major economic implications for horse breeders, and despite there being many studies focusing on conception and embryo loss, the mechanisms by which the uterus is primed for pregnancy are yet to be elucidated in this species. To advance knowledge in this space, the present study aimed to characterise the transcriptome of epithelial glands derived from the equine endometrium. Two endometrial tissue samples were collected from two mares immediately post-mortem, and epithelial gland cells were isolated via enzymatic digestion. Contaminating stromal cells were removed by selective adhesion. RNA was isolated from purified gland cells before being sequenced using DNB-Seq technology. Epithelial gland cell sequencing data were analysed at SAHMRI and bioinformatics analysis was completed using protein analysis through evolutionary relationships (PANTHER). A total of 13,038 unique genes were identified by RNA-Seq with >2 counts per million (CPM) in each sample. Amongst the most abundant protein-coding genes were MT-CO1, EEF1A1, EGR1, HSP90AA1 and CD74, with roles in cellular respiration, translation, transcription regulation and the innate immune system, respectively. PANTHER analysis revealed 157 active pathways, the most prominent being Wnt signalling, chemokine and cytokine mediated inflammation, GNRH receptivity, integrin signalling and angiogenesis. Additionally, biological functions associated with the immune system and reproduction comprised 2.3% and 0.6% of the identified genes respectively. In conclusion, this study is the first to characterise the transcriptome of equine epithelial gland cells and provides novel insights into the functions of genes expressed in this cell type. These findings establish a foundation for the development of novel in vitro models, such as a 3-dimensional endometrial organoid model, required for the advancement of knowledge surrounding uterine priming and conception in the mare.