Precise control over signal amplification provides unparalleled opportunities for diverse applications. However, spatiotemporally controlled amplification has not been realized because of the lack of a design methodology. The aim of this study was thus to develop a conceptual approach for remote control over signal amplification at a chosen time and site in living cells. This system was constructed by re-engineering the functional units of the hybridization chain reaction (HCR) and combination with upconversion photochemistry, thus resulting in an activatable HCR with the high spatial and temporal precision of near-infrared (NIR) light. As a proof of concept, we demonstrate the spatially and temporally resolved amplified imaging of messenger RNA (mRNA) with ultrahigh sensitivity in vitro and in vivo. Furthermore, by using a system targeting subcellular sites we have developed a new technique for NIR-initiated amplified imaging of mRNA exclusively within a specific organelle.