The chicken chorioallantoic membrane (CAM) is an extraembryonic structure that exhibits many vital functions to support the development of the chicken embryo (gaseous exchange, innate defence, calcium transport from the eggshell to the embryo skeleton, homeostasis). Developing from day 6 of incubation, the CAM progressively differentiates into three functional layers (the chorionic epithelium in contact with the inner eggshell, the highly vascularized mesoderm, and the allantoic epithelium), between 11 and 15 days of incubation. This article describes the RNASeq dataset and the analyses performed on total CAMs collected from male and female embryos after 11 and 15 days of incubation. The datasets are available at the NCBI Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo) using GSE199780 as the accession number. The statistical analysis of the data allowed identifying genes differentially expressed depending on the sex of the embryo at two time points of CAM differentiation. Knowing that the CAM is widely used as a model to study tumour growth, metastasis or wound healing, the resulting analysis highlights the necessity to include this sex variable in experimental assays to avoid any bias of interpretation. Indeed, the functional annotation of genes that are differentially expressed between male and female CAMs revealed an enrichment of activities and functions related to lipid metabolism, bone formation, and morphogenesis suggesting that the response of the CAM to external and experimental stimuli might be different depending on the sex of the embryo.