Native nanoelectrospray ionization mass spectrometry is an underutilized technique for fragment screening. In this study, the first demonstration is provided of the use of native mass spectrometry for screening fragments against a protein–DNA interaction. EthR is a transcriptional repressor of EthA expression in Mycobacterium tuberculosis (Mtb) that reduces the efficacy of ethionamide, a second‐line antitubercular drug used to combat multidrug‐resistant Mtb strains. A small‐scale fragment screening campaign was conducted against the EthR–DNA interaction using native mass spectrometry, and the results were compared with those from differential scanning fluorimetry, a commonly used primary screening technique. Hits were validated by surface plasmon resonance and X‐ray crystallography. The screening campaign identified two new fragments that disrupt the EthR–DNA interaction in vitro (IC50=460–610 μm) and bind to the hydrophobic channel of the EthR dimer.