Activation of c-Jun, a major component of the AP-1 transcription factor, represents a paradigm for transcriptional response to stress. Transactivation of c-Jun is regulated by Jun-N-terminal kinases (JNKs) through phosphorylation at serine 63 and 73 (S63/S73), as well as at threonine 91 and 93 (T91/T93). How these two groups of phosphoacceptor sites respond to different grades of genotoxic stress and whether DNA-damage pathways influence the extent of their JNK-dependent phosphorylations remain to be elucidated. Here, we show that following a short exposure to the DNA-damaging compound etoposide, c-Jun phosphorylation is restricted to S63/S73. In contrast, JNK-dependent phosphorylation of T91/T93 requires continuous exposure to the drug and is impaired by caffeine treatment or alanine substitution of the adjacent threonine 95 (T95). Conversely, c-Jun mutations switching the T95/Q96 site into a canonical site for mitogen activated protein kinase (MAPK) phosphorylation (T95/P96) rescues T91/T93 phosphorylation in presence of caffeine, suggesting that a preceding phosphorylation at T95 exposes T91/T93 to JNK-dependent phosphorylation. Moreover, we show that alanine substitution at T95 impairs c-Jun transactivation and c-Jun-mediated cell death, indicating that negatively charged T95 is a general constraint for c-Jun activation. Hence, our study suggests that c-Jun may sense the strength of genotoxic stress through DNA-damage dependent phosphorylation of T95, which in turn augments c-Jun transactivation by JNKs.