Transposable elements (TE) function as one of the major effectors to respond to biological or environmental stress. The mobility of TEs, which is heavily controlled under normal conditions, may be activated by stress. LncRNAs are emerging as a crucial tool in the regulation of TEs. This study focuses on the gene expression of THAP9, a domesticated transposon and lncRNA THAP9-AS1 (THAP9-antisense1), which form a sense and antisense gene pair with a promoter overlap of approximately 350bp. Under basal conditions, THAP9 is preferentially transcribed while THAP9-AS1 is heavily down-regulated. In the S-phase of the cell cycle, THAP9 expression exhibits stress-specific effects ranging from moderate enhancement to no change. On the other hand, THAP9-AS1, which has previously been reported to be upregulated in several cancers, always demonstrates enhanced expression under stress. Moreover, THAP9-AS1 is transcriptionally favoured during stress since the stress-induced fold-increase of THAP-AS1 expression is always higher than THAP9. Interestingly, the expression of both THAP9 and THAP9-AS1 exhibit a striking periodicity throughout the S-phase, reminiscent of cell cycle regulated genes. Thus, this study sets the stage to further explore the relationship between THAP9 and THAP9-AS1 and investigate THAP9-AS1’s potential regulatory role during stress.