In many cells, thiol-based redox systems are primarily responsible for hydrogen peroxide reduction but also trigger signalling cascades leading to the induction of oxidant-specific transcriptional programs by redox-sensitive transcription factors. Cells lacking these transcription factors are extremely sensitive to oxidative stress, but their constitutive activation is also detrimental. However, the quantitative relationship between these oxidative inputs and transcriptional outputs has remained obscure because we lacked tools to quantify the dynamics of redox signals. Using the fission yeast Pap1 transcription factor pathway as a model, we show how hydrogen peroxide and tert-butyl hydroperoxide triggered quantifiably distinct Pap1 activation profiles and transcriptional responses. Based on these findings, we propose that different oxidants and oxidant concentrations modulate the Pap1 dynamic profile, leading to specific transcriptional responses. We further show how the effect of combination and pre-exposure stresses on Pap1 activation dynamics can be quantified using this approach. Our work advances the concept that redox signalling dynamics are a key aspect of the oxidative stress response.