Nowadays, zinc oxide nanoparticles (ZnO NPs) have been shown to exhibit potent antibacterial activity against a wide range of pathogenic bacteria. Numerous investigations have delved into exploring the antibacterial activities exhibited by ZnO NPs. Notwithstanding, the correlation between the morphology of these nanoparticles and their resultant antibacterial impacts remains an area demanding further exploration across varying morphological variations. This paper presents a comparative study on how the morphology of zinc oxide nanoparticles affects their antibacterial efficacy. In this regard, ZnO NPs with different morphologies, including spherical, rod-like, and flower-like structures, were synthesized via a modified precipitation method and characterized using X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, thermogravimetric analysis (TGA), field emission scanning electron microscopy (FE-SEM), dynamic light scattering (DLS), Brunauer−Emmett−Teller (BET) analysis, and reactive oxygen species (ROS) analysis techniques. The antibacterial activity of these nanoparticles was evaluated against a Gram-positive bacterium (Staphylococcus aureus) and two Gramnegative bacteria (Escherichia coli and Pseudomonas aeruginosa) through disk diffusion, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) tests, and their cytotoxicity was assessed using the MTT assay. The results showed that the ZnO NPs with rod-like morphology exhibited the highest antibacterial activity against both Gram-positive and Gramnegative bacteria. Conversely, the spherical NPs displayed the lowest antibacterial activity. Remarkably, the cytotoxicity assessments showed that the spherical nanoparticles exerted the highest toxicity toward HepG2 and human dermal fibroblasts (HDF) cells, whereas the rod-like NPs demonstrated the least cytotoxic effects. The extent of cell membrane damage was determined by measuring DNA and RNA leakage, with visual confirmation through FESEM imaging. The results of this study provide valuable insights into the relationship between zinc oxide nanoparticle morphology and antibacterial efficacy, shedding light on the mechanisms underlying the superior antibacterial activity of a rod-like morphology. Overall, the findings provide valuable insights into designing and developing efficient antibacterial agents with minimal adverse effects, opening up avenues for future research in nanomedicine and biomedical applications.