Introduction: Understanding how transcranial magnetic stimulation (TMS) interacts with cortical circuits is enhanced by application of biophysical models. Population-based models of cortical activity have captured plasticity responses due to TMS, but these have not calculated changes in motor-evoked potentials (MEPs), standard electromyographic measures inferring the cortical response to TMS.Objectives: To develop a population-based biophysical model of MEPs following TMS.Methods: We use an existing MEP model in conjunction with population-based modeling of the cortex. We consider populations of layer 2/3 excitatory and inhibitory neurons, stimulated by TMS pulses. These populations feed a population of layer 5 corticospinal neurons, with both excitatory and inhibitory connections. The layer 5 population also couples directly but weakly to the TMS pulses. The layer 5 output controls the mean motoneuron response, and from that a series of single motounit action potentials are generated and summed to give a MEP.Results: A realistic MEP waveform was generated by the model comparable to those observed in real experiments. The model captured TMS phenomena including a sigmoidal shaped input-output curve with increasing stimulation intensity, common paired-pulse effects (SICI, ICF, LICI) including responses to pharmacological interventions, and a cortical silent period. Changes in MEP amplitude following theta burst paradigms were also observed including variability in outcome direction.Conclusions: The model enables better interpretation of population-based TMS modeling approaches by interpreting output in terms of MEPs, thus providing a quantitative link between the cortical circuits activated by TMS and functional outcomes.