A method based on a multicommutation stopped-flow system was developed and applied in the simultaneous determination of sulfamethoxazole (SMX) and trimethoprim (TMP) in pharmaceutical formulations by differential pulse voltammetry (DPV) using a cathodically pre-treated hydrogen-terminated boron-doped diamond (HT-BDD) electrode. The obtained analytical curves were linear from 1.0 to 8.0 mg L(-1) and 0.20 to 1.6 mg L(-1) for SMX and TMP, respectively. The calculated LOD and LOQ values for SMX were 16.5 mu g L(-1) and 55.1 mu g L(-1) (or 65.1 nmol L(-1) and 218 nmol L(-1)), respectively; for TMP, they were 18.3 mu g L(-1) and 61.1 mu g L(-1) (or 63.0 nmol L(-1) and 210 nmol L(-1)), respectively. The optimization and application of the multicommutation stopped-flow system in the simultaneous electrochemical determination of SMX and TMP by DPV on the HT-BDD electrode yielded an excellent sample throughput (30 h(-1)). Addition and recovery studies indicated that the matrix effect did not present any significant interference in the determinations. Thus, the proposed method was successfully applied in the determination of SMX and TMP in two different commercial pharmaceutical formulations with results similar (at 95% confidence level) to those obtained using the USP method (HPLC). The obtained performance allowed concluding that the proposed method is quite advantageous and that its total automation can lead to rapid, sensitive, precise, and accurate results, with an excellent sample throughput.