Quantum cascade lasers are coherent light sources that rely on intrersubband transition in periodic semiconductor quantum well structures. They operate at frequencies from mid-infrared to terahertz. In cases of long wavelength and typical low thermal conductivity of the active region, temperature rise in the active region during operation is a major concern. Thermal conductivity of QCL epi-layers differ significantly from the values of bulk semiconductors and measurement of the thermal conductivity of epi-layers is critical for design. It is well known that Fabry-Perot spectra of QCL cavities exhibit fine amplitude oscillations with frequency and can be used for real time in-situ temperature measurement. Phase of the modulation depends on the group refractive index of the cavity, which depends on the cavity temperature. We fabricated QCL devices with from 12, to 24 um mesa widths and 2mm cavity length and and measured high resolution, high speed time resolved spectra using a FTIR spectrometer in step scan mode in a liquid nitrogen cooled, temperature controlled dewar. We used the time resolved spectra of QCLs to measure average temperature of the active region of the laser as a function of time. We examined the effect of pulse width and duty cycle on laser heating. We measured the temperature derivative of group refractive index of the cavity. Building a numerical model, we estimated the thermal conductivity of active region and calculated the heating of the QCL active region in pulsed mode for various waveguide widths.