Temperature rise during operation is a central concern of semiconductor lasers and especially difficult to measure during a pulsed operation. We present a technique for in situ time-resolved temperature measurement of quantum cascade lasers operating in a pulsed mode at ~9.25 μm emission wavelength. Using a step-scan approach with 5 ns resolution, we measure the temporal evolution of the spectral density, observing longitudinal Fabry-Perot modes that correspond to different transverse modes. Considering the multiple thin layers that make up the active layer and the associated Kapitza resistance, thermal properties of QCLs are significantly different than bulk-like laser diodes where this approach was successfully used. Compounded by the lattice expansion and refractive index changes due to time-dependent temperature rise, Fabry-Perot modes were observed and analyzed from the time-resolved emission spectra of quantum cascade lasers to deduce the cavity temperature. Temperature rise of a QCL in a pulsed mode operation between -160 °C to -80 °C was measured as a function of time. Using the temporal temperature variations, a thermal model was constructed that led to the extraction of cavity thermal conductivity in agreement with previous results. Critical in maximizing pulsed output power, the effect of the duty cycle on the evolution of laser heating was studied in situ, leading to a heat map to guide the operation of pulsed lasers.