Cells from yeast to humans activate unconventional mRNA splicing when unfolded proteins accumulate in the endoplasmic reticulum (ER) under ER stress conditions. The substrate of this splicing in mammalian cells is XBP1 mRNA, which encodes the unfolded protein response (UPR)-specific transcription factor XBP1. The C-terminal region of XBP1 is switched as a result of the splicing. Thus, unspliced and spliced mRNAs produce pXBP1(U) of 261 aa and pXBP1(S) of 376 aa, respectively, with the N-terminal region containing the DNA-binding domain shared. As the pXBP1(S)-specific C-terminal region functions as an activation domain, pXBP1(S) can activate transcription efficiently. We recently found that pXBP1(U) shuttles between the nucleus and cytoplasm, owing to the presence of a nuclear exclusion signal in the pXBP1(U)-specific C-terminal region, in marked contrast to the exclusively nuclear localization of pXBP1(S). pXBP1(U) can associate with pXBP1(S), and pXBP1(U)-pXBP1(S) complex is rapidly degraded by the proteasome. Two other transcription factors are activated in response to ER stress, namely ATF6 and ATF4. ATF6 is a UPR-specific transcription factor, whereas ATF4 is activated by not only ER stress but also various other stimuli. In this study, we show that pXBP1(U) targets the active form of ATF6 but not ATF4 for destruction by the proteasome via direct association. This enhanced degradation is mediated by the degradation domain located at the pXBP1(U)-specific C-terminal end. We conclude that pXBP1(U) functions as a negative regulator of the UPR-specific transcription factors ATF6 and pXBP1(S).