In recent years, the advances in terahertz applications have stimulated interest in the biological effects associated with this frequency range. We study the gene expression profile in three types of cells exposed to terahertz radiation, i.e., human ARPE-19 retinal pigment epithelial cells, simian virus 40-transformed human corneal epithelial cells, and human MIO-M1 Müller cells. We find that the gene expression in response to heat shock is unaffected, indicating that the minimum temperature increases under controlled environment. The transcriptome sequencing survey demonstrates that 6-hour irradiation with a broadband terahertz source results in specific change in gene expression and also the biological functions that are closely related to these genes. Our results imply that the effect of terahertz radiation on gene expression can last over 15 hours and depends on the type of cell.