Variation in growth conditions is an inevitable consequence of the environment’s dynamism and, as such, organisms are subjected to adverse living conditions including non-optimal temperature. Exposure to elevated temperature and other proteotoxic stresses disrupts structural integrity of cellular machineries and results in cytotoxic unfolded-protein-aggregates. To cope with proteotoxic stresses, organisms are equipped with an evolutionarily conserved defense mechanism known as heat shock response (HSR). Despite the significance of HSR in protein homeostasis and survival, it’s scope, extent, and the molecular mechanism of regulation are poorly understood. Our work shows that the genome-wide transcriptional response to heat-stress in mammals is rapid, dynamic, and results in induction of several hundred and repression of several thousand genes. Heat shock factor 1 (HSF1), ‘the master regulator’ of the HSR, controls only a fraction of the heat-stress induced genes, and does so by increasing RNA polymerase II (Pol II) release from its promoter-proximal pause. The pervasive repression of transcription is predominantly HSF1-independent, and is mediated through reduction of Pol II pause-release. The up- and down-regulated genes during HSR are accompanied by concomitant increase and decrease respectively in promoter occupancy of pause-release factor positive transcription elongation factor b (P-TEFb). HSF2, the ubiquitously expressed paralog of HSF1, has a broader repressive role during stress, likely mediated through other factors, and its promoter-binding activity is dependent on HSF1. Our work also demonstrates the unprecedented role of serum response factor (SRF) in transient induction of cytoskeletal genes during the early phase of HSR. Overall, mammalian cells orchestrate rapid, dynamic, and extensive changes in transcription upon heat-stress that are largely modulated at pause-release, and HSF1 plays a limited and specialized role.