Hydroxyapatite (HA) and β-tricalcium phosphate (β-TCP) represent the main types of calcium phosphates used for bone and dental surgery. Zinc is the most abundant trace metallic element found in bone, and essential metal that plays a crucial role in the biochemistry of bone tissues. Therefore, Zn doped biphasic calcium phosphate (Zn-BCP) can be a good choice of biomaterial for bone repair and regeneration. These compositions were prepared via simple sol–gel route. The aim of this work was to evaluate the antibacterial effect of Zn-BCP (1.6, 3.2 wt%Zn) nanopowders. X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), Fourier transformer infrared spectrophotometer (FTIR) and inductive coupled plasma-atomic emission spectroscopy (ICP-AES) were used for characterization and evaluation of the phase composition, morphology and particle size of the products. The size of the prepared nanoparticles was measured between 10–500 nm. The antibacterial activity was evaluated by using Escherichia coli and Salmonella typhi as gram negative, and Staphylococcus aureus as gram-positive bacteria. The antibacterial effect of the samples was investigated at concentration of 100, 200 and 300 mg/ml. Neither of them showed any antibacterial activity at 100 mg/ml concentration. At concentrations of 200 and 300 mg/ml of the broth, the Zn-BCP with 1.6 wt% Zn had no antibacterial effect. However, Zn-BCP with 3.2 wt% Zn had considerable antibacterial activity.