The objective of this work was to synthesize molecularly imprinted polymer (MIP) nanoparticles based on methacrylic acid (MAA) monomer with a high selectivity against an anti-cancer drug, 5-fluorouracil (5-FU), as a template. In this case, the nanoparticles were prepared via precipitation polymerization in the presence of ethylene glycol dimethacrylate as cross-linker and azobisisobutyronitrile as initiator. Besides, 3 independent variables including MAA: 5-FU molar ratio (X 1 ), temperature (X 2 ), and time (X 3 ) were investigated utilizing response surface methodology. The scanning electron microscopy and dynamic light scattering resulted the average diameter of approximately 65 nm, and the MIP nanoparticle sample with the imprinting factor of 1.57 was polymerized in optimized conditions as follows: X 1 = 6: 1, X 2 = 60°C, and X 3 = 3 days in acetonitrile as porogenic solvent. Also, Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis confirmed the formation of MAA/5-FU complex and lower thermal stability of the washed MIP sample than the unwashed MIP and non-imprinted polymer (NIP) samples, respectively. Moreover, the optimized MIP nanoparticles have more controlled release of 5-FU rather than the NIP sample. Finally, the flow cytometry showed that 5-FU-loaded MIP sample has the highest apoptosis of human colon cancer cell line, HCT-116, after 3 days compared with NIP sample and also the exclusive use of drug.