The emerging resistance of tuberculosis (TB) to current first line drugs (isoniazid, rifampicin, pyrazinamide, ethambutol) warrants alternative treatment approaches with broad-spectrum efficacy. Previously, we have shown that sulfamethoxazole (SMX) has synergestic activity with rifampicin against Mycobacterium tuberculosis. The primary target of SMX is folP1 in mycobacteria; however, SMX may affect other secondary targets in M. tuberculosis. This study investigated the potential additional targets of SMX in a clinical isolate of M. tuberculosis using Orbitrap mass spectrometry to identify differentially expressed proteins following treatment with a sub-lethal concentration of SMX. Raw data have been deposited as ProteomeXchange accession PXD009315. Our proteomic analysis identified approximately 1500 proteins in total of which 45 proteins were differentially regulated as a result of SMX treatment. These included 25 upregulated and 20 downregulated proteins. The oxidative stress proteins (Rv2428, AhpC and Rv2394, GgtB) and an enzyme from the electron transport chain (Ndh-II, Rv1854c) were found to be upregulated. Gene expression analysis correlated with the observed proteomic changes. In conclusion our results show that SMX treatment of a drug sensitive M. tuberculosis clinical isolate resulted in the regulation of proteins involved in the oxidative stress response, indicating the induction of oxidative stress by SMX in mycobacteria.