It is evident that preparing materials, casting samples, curing, and testing all need time and money. The construction sector will benefit if these problems can be handled using cutting-edge techniques like machine learning. Also, a material’s ultrasonic pulse velocity (UPV) is affected by various variables, and it is difficult to study their combined effect experimentally. This research used machine learning to assess the UPV and SHapley Additive ExPlanations techniques to study the impact of input parameters of hybrid fiber-reinforced concrete modified with nano-silica (HFRNSC). Three ML algorithms were employed, i.e., gradient boosting regressor, adaptive boosting regressor, and extreme gradient boosting, for ultrasonic pulse velocity evaluation. The accuracy of machine learning models was measured via the coefficient of determination (R2), k-fold analysis, statistical tests, and comparing the predicted and actual ultrasonic pulse velocity. This study determined that the gradient boosting and adaptive boosting models had a good level of accuracy for ultrasonic pulse velocity, but the extreme gradient boosting method estimated the ultrasonic pulse velocity of HFRNSCs with a greater degree of precision. Also, from the statistical checks and k-fold approach, it was discovered that the extreme gradient boosting method is more exact in estimating the ultrasonic pulse velocity of HFRNSCs. The SHapley Additive ExPlanations analysis revealed that the age of the specimen and nano-silica had a greater positive impact on the ultrasonic pulse velocity of HFRNSCs, whereas the coarse aggregate to fine aggregate ratio had a negative impact. In addition, fiber volume was found to have both positive and negative effects. By aiding the development of rapid and low-cost methods for determining material properties and the influence of input parameters, the construction industry may profit from the use of such technologies.