Epidermal growth factor‑like domain 8 (EGFL8), a newly identified member of the EGFL family, and plays negative regulatory roles in mouse thymic epithelial cells (TECs) and thymocytes. However, the role of EGFL8 in these cells remains poorly understood. In the present study, in order to characterize the function of EGFL8, genome‑wide expression profiles in EGFL8‑overexpressing or ‑silenced mouse cortical TECs (cTECs) were analyzed. Microarray analysis revealed that 458 genes exhibited a >2‑fold change in expression levels in the EGFL8‑overexpressing vs. the EGFL8‑silenced cTECs. Several genes involved in a number of cellular processes, such as the cell cycle, proliferation, growth, migration and differentiation, as well as in apoptosis, reactive oxygen species generation, chemotaxis and immune responses, were differentially expressed in the EGFL8‑overexpressing or ‑silenced cTECs. WST‑1 analysis revealed that that the overexpression of EGFL8 inhibited cTEC proliferation. To investigate the underlying mechanisms of EGFL8 in the regulation of cTEC function, genes related to essential cellular functions were selected. Reverse transcription‑polymerase chain reaction analysis revealed that EGFL8 knockdown upregulated the expression of cluster differentiation 74 (CD74), Fas ligand (FasL), C‑X‑C motif chemokine ligand 5 (CXCL5), CXCL10, CXCL16, C‑C motif chemokine ligand 20 (CCL20), vascular endothelial growth factor‑A (VEGF‑A), interferon regulatory factor 7 (Irf7), insulin‑like growth factor binding protein‑4 (IGFBP‑4), thrombospondin 1 (Thbs1) and nuclear factor κB subunit 2 (NF‑κB2) genes, and downregulated the expression of angiopoietin‑like 1 (Angptl1), and neuropilin‑1 (Nrp1) genes. Additionally, EGFL8 silencing enhanced the expression of anti‑apoptotic molecules, such as B‑cell lymphoma‑2 (Bcl‑2) and Bcl‑extra large (Bcl‑xL), and that of cell cycle‑regulating molecules, such as cyclin‑dependent kinase 1 (CDK1), CDK4, CDK6 and cyclin D1. Moreover, gene network analysis revealed that EGFL8 exerted negative effects on VEGF‑A gene expression. Hence, the altered expression of several genes associated with EGFL8 expression in cTECs highlights the important physiological processes in which EGFL8 is involved, and provides insight into its biological functions.