This paper compares the noise performance of two different types of time-domain microwave detection systems: a pulsed system and a pseudo-random noise sequence system. System-level simulations and laboratory-based measurements are carried out in the study. Results show that the effect of timing jitter is more significant on the measurement accuracy of the pseudo-random noise sequence system than that of the pulsed system. Although the signal power density of the pseudo-random sequence system is tens of dBs higher than that of the pulsed system over the frequency band of interest, the signal-to-noise ratio difference between these two systems can be just a few dBs or even smaller depending on the jitter level.