We investigate numerically the thermoelectric properties of aperiodic graphene superlattices generated by applying an external electric field following the Fibonacci and Thue–Morse sequences. We find that aperiodicity reduces and fragments the transmission bands natural in periodic superlattices as well as redistributes the density of states of the system. We also find an overall reduction of the conductance in aperiodic graphene superlattices with respect to periodic ones. Furthermore, as the generation of the aperiodic structure increases, the conductance decreases and a series of peaks arise on it. This behavior is more pronounced in Thue–Morse superlattices than in Fibonacci ones. In the case of the thermoelectric properties, we obtain that Fibonacci graphene superlattices present similar values for the Seebeck coefficient and the power factor as in periodic superlattices, while Thue–Morse graphene superlattices show an enhancement of the thermoelectric properties, in particular the power factor is two times larger than the corresponding one to periodic and Fibonacci graphene superlattices. So, according to our findings, aperiodicity can be used as a tuning parameter to improve the thermoelectric properties of graphene superlattices.