Speed of sound (SoS) is an acoustic property that is highly sensitive to changes in tissues. SoS can be mapped non-invasively using ultrasonic through transmission wave tomography. This however, practically limits its clinical use to the breast. A pulse-echo-based method that has broader clinical use and that can reliably measure treatment-induced changes in SoS even under poor signal-to-noise ratio (SNR) is highly desirable. The aim of this study was to evaluate the implementation of coded excitations (CoEs) to improve pulse-echo monitoring of heat-induced changes in the SoS. In this study, a binary phase modulated Barker sequence and a linear frequency-modulated chirp were compared with a common Gaussian pulse transmission. The comparison was conducted using computer simulations, as well as transmissions in both agar-gelatin phantoms and ex vivo bovine liver. SoS changes were experimentally induced by heating the specimens with a therapeutic ultrasound system. The performance of each transmission signal was evaluated by correlating the relative echo shifts to the normalized SoS measured by through transmission. The computer simulations indicated that CoEs are beneficial at very low SNR. The Barker code performed better than both the chirp and Gaussian pulses, particularly at SNRs <10 dB (R2 = 0.81 ± 0.06, 0.68 ± 0.07 and 0.55 ± 0.08, respectively, at 0 dB). At high SNRs, the CoEs performed statistically on par with the Gaussian pulse. The experimental findings indicated that both Barker and chirp codes performed better than the Gaussian pulse on ex vivo liver (R2 = 0.80 ± 0.15, 0.79 ± 0.15 and 0.54 ± 0.17, respectively) and comparably on agar-gelatin phantoms. In conclusion, CoEs can be beneficial for assessing temperature-induced changes in the SoS using the pulse-echo method under poor SNR.