A technique for the accurate computation of the time domain electromagnetic fields radiated by a charged distribution traveling along an arbitrarily shaped waveguide region is presented. Based on the transformation (by means of the standard Fourier analysis) of the time-varying current density of the analyzed problem to the frequency domain, the resulting equivalent current is further convolved with the dyadic electric and magnetic Green's functions. Moreover, we show that only the evaluation of the transverse magnetic modes of the structure is required for the calculation of fields radiated by particles traveling in the axial direction. Finally, frequency domain electric and magnetic fields are transformed back to the time domain, just obtaining the total fields radiated by the charged distribution. Furthermore, we present a method for the computation of the wakefields of arbitrary cross-section uniform waveguides from the resulting field expressions. Several examples of charged particles moving in the axial direction of such waveguides are included.