We have previously shown analytically that the biologically effective dose (BED), including effects of repair during irradiation and of incomplete repair between fractions, can be formulated using a convolution between the absorbed dose rate function and the function describing repair. In this work, a discrete formalism is derived along with its implementation via the fast Fourier transform. The implementation takes the intrinsic periodicity of the discrete Fourier transform into consideration, as well as possible inconsistencies that may arise due to discretization and truncation of the functions describing the absorbed dose rate and repair. Numerically and analytically calculated BED values are compared for various situations in external beam radiotherapy, brachytherapy and radionuclide therapy, including the use of different repair models. The numerical method is shown to be accurate and versatile since it can be applied to any kind of absorbed dose rate function and allows for the incorporation of different repair models. Typical accuracies for clinically realistic examples are in the order of 10(-3)% to 10(-5)%. The method has thus the potential of being a useful tool for the calculation of BED, also in situations with complicated irradiation patterns or repair functions.