Diagnosis of cancer by chemotherapy treatment, severe side effects caused by high dosages of cancer drugs include non-controlled cytotoxicity to bone marrow cells and immune cells. To overcome, we have synthesized nanoparticles with controlled sized hydroxyapatite (nHAp) materials doped and co-doped with silver and iron by co-precipitation, yielding materials that can treat both the infections and malignant tumors with non-cytotoxic nature to normal cells. Spherical and rod like morphologies were observed for the samples with higher Ag doping concentrations with average size of 50 ± 5 nm and (75 × 22) ± 5 nm, whereas higher Ag/Fe co-doping concentrations yielded samples with spherical, rod-like, and flake-like structures. For samples nHAp and Ag-nHAp samples were diamagnetic, whereas the Fe-nHAp and Ag/Fe co-doped samples were superparamagnetic. The in vitro biological toxicity study revealed that the Ag/Fe-nHAp nanoparticles are effective for targeting to kill cancerous cells, for example, human cervical cancer (HeLa) cells efficiently while they are non-toxic to normal cells. Applying these nanoparticles for drug delivery system, 5-fluorouracil was loaded in the nanoparticles and studied its release kinetics. In the case of Ag/Feco-doped nHAp samples, a pulsatile drug release profile was observed, which the drug was released for about a week on varying the Ag and Fe concentrations. The 5-fluorouracil release kinetics was well fitted by the first-order model with diffusion. Thus, nHAps co-doped with Ag/Fe material have the potential to lag the time on delivering the drug at site-specific could be with an application in biomedicine such as to treat malignant tumor without any bacterial side effect.