Host cell entry of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is facilitated via priming of its spike glycoprotein by the human transmembrane protease serine 2 (TMPRSS2). Although camostat and nafamostat are two highly potent covalent TMPRSS2 inhibitors, they nevertheless did not hold promise in COVID‐19 clinical trials, presumably due to their short plasma half‐lives. Herein, we report an integrative chemogenomics approach based on computational modeling and in vitro enzymatic assays, for repurposing serine‐targeted covalent inhibitors. This led to the identification of BC‐11 as a covalent TMPRSS2 inhibitor displaying a unique selectivity profile for serine proteases, ascribable to its boronic acid warhead. BC‐11 showed modest inhibition of SARS‐CoV‐2 (omicron variant) spike pseudotyped particles in a cell‐based entry assay, and a combination of BC‐11 and AHN 1‐055 (a spike glycoprotein inhibitor) demonstrated better viral entry inhibition than either compound alone. Given its low molecular weight and good activity against TMPRSS2, BC‐11 qualifies as a good starting point for further structural optimizations.