In this paper, an uncertainty-aware task scheduling approach capable of dynamically applying on multiprocessor embedded systems called ”DyUnS” is presented. This method is based on a type-2 fuzzy inference system to consider all design challenges of multiprocessor embedded systems along with their unavoidable uncertainty caused by the differences in models and measurements. The proposed method employs a fuzzy inference system to approximate the appropriate assignment of the application’s tasks to processing cores based on a defined rank including the main design challenges of the system including execution time, temperature, power consumption, and reliability. Moreover, an uncertainty level is defined for various design challenges as the footprint of uncertainty during the scheduling process to tackle the existing inaccuracy between the static models and dynamic environment. Thus, the generated uncertainty-aware solution could be efficiently employed as a dynamic scheduling at runtime. To demonstrate the effectiveness of DyUnS in tolerating uncertainty, several experiments on various application graphs are performed and its effectually is compared to related studies. Based on these experiments, DyUnS jointly optimizes the main design parameters, and its generated solution could be employed dynamically without violating the system’s thresholds. Moreover, its average difference compared to Monte Carlo uncertainty analysis is about 0.2 for all design parameters in three levels of uncertainty.