The development of non-antibiotic based treatments against bacterial infections by Gram-negative uropathogenic E. coli is a complex task. New strategies to treat such infections are thus urgently needed. This report illustrates the development of pegylated reduced graphene oxide nanoparticles (rGO-PEG) and gold nanorods (Au NRs) coated with rGO-PEG (rGO-PEG-Au NRs) for the selective killing of uropathogenic E. coli UTI89. We took advantage of the excellent light absorption properties of rGO-PEG and Au NR particles in the near-infrared (NIR) region to photothermally kill Gram-negative pathogens up to 99% in 10 min by illumination of solutions containing the bacteria. The rGO-PEG-Au NRs demonstrated better photothermal efficiency towards E. coli than rGO-PEG. Targeted killing of E. coli UTI89 could be achieved with rGO-PEG-Au NRs functionalized with multimeric heptyl α-d-mannoside probes. This currently offers a unique biocompatible method for the ablation of pathogens with the opening of probably a new possibility for clinical treatments of patients with urinary infections.