1,4‐Naphthoquinones are an important class of compounds present in a number of natural products. In this study, a new series of 1,4‐naphthoquinone derivatives were synthesized. All the synthesized compounds were tested for
in vitro
antimicrobial activity. In this present investigation, two Gram‐positive and five Gram‐negative bacterial strains and one pathogenic yeast strain were used to determine the antibacterial activity. Naphthoquinones tested for its antibacterial potencies, among seven of them displayed better antimicrobial activity against
Staphylococcus aureus
(
S. aureus
; 30–70 μg/mL). Some of the tested compounds showed moderate to low antimicrobial activity against
Pseudomonas aeruginosa
(
P. aeruginosa
) and
Salmonella bongori
(
S. bongori
; 70–150 μg/mL). In addition, most active compounds against
S. aureus
were evaluated for toxicity to human blood cells using a hemolysis assay. For better understanding, reactive oxygen species (ROS) generation, time‐kill kinetic study, and apoptosis, necrosis responses were investigated for three representative compounds.