The study of annular thermoelectric generators (ATEG) has attracted more attention in recent years due to their ability to cover round shaped surfaces. Moreover, transient and pulsed inputs have been introduced as some of the effective methods to enhance the performance of thermoelectric devices. Hence, in the present study, a three-dimensional transient simulation of ATEG including the influence of Thomson effect is carried out based on finite element method. The effect of pulsed heat inputs on the performance of ATEG is studied considering rectangular, triangular, sinusoidal and two types of the sawtooth input functions for modeling the transient heat load. Electric current, voltage, output power and conversion efficiency of ATEG under pulsed and steady-state heating are compared. The effects of two critical parameters, the ratio of maximum heat flux to minimum heat flux (b/a) and duty cycle (t(0)/tau) values on the performance of ATEG are studied. Results indicate that transient pulsed heating enhances the efficiency of ATEG for all types of heat input functions. In addition, it is found that rectangular input function leads to better results compared to other functions. Also, it is shown that for a constant amount of duty cycle, the increment of (b/a) increases the performance of ATEG unit. For duty cycle value of 0.1 and (b/a = 48) a maximum efficiency enhancement of 249.36% is achieved when the rectangular input function is employed. It is found that in the range of the studied values of (b/a), the duty cycle of 0.4 leads to better results. A comparison of results with and without Thomson effect proves that the Thomson effect decreases the performance of ATEG. Additionally, it is observed that for sawtooth input functions, the implementation of heat load gradient plays an important role determining the performance.