Neisseria gonorrhoeae (GC) is the agent of one of the most common bacterial sexually transmitted infections worldwide. The possible development of 'untreatable' infections points out the need for antibiotic-sparing methods to reduce the number of gonococcal infections. In this context, fatty acids are interesting candidates as next-generation antibacterial agents. The aim of this study was to investigate the bactericidal effects of selected fatty acids on GC viability, as well as to observe their biological effects by means of transmission electron microscopy. The cytotoxicity of these compounds on human cervical cells (HeLa), chosen as a model of genital mucosa, was assessed as well. Lauric, myristic, and palmitic acid displayed high killing activity against GC in concentrations ranging between 100 μM and 25 μM, whereas the antimicrobial effect of oleic and butyric acids was present in concentrations between 1 mM and 0.25 mM. Modifications induced by fatty acids on the GC cell included the disorganization of the cytoplasmic structure, the distortion of pili/fimbriae, and the separation of the inner and outer membrane layers. For concentrations active against GC, fatty acids were not toxic for cervical cells. Our data can help in promoting innovative antibiotic-free compounds for the treatment of GC infections.