Nanoscale devices offer a lot of potential in drug delivery because of their small size. The goal of this work was to increase the oral bioavailability of the anti-cancer hydrophilic drug as 5-fluorouracil (5-FU) by incorporating it into poly (D, L-lactide-co-glycolide) nanoparticles (PLGNPs) using the double emulsion process, 5-FU- PLGNPs nanoparticles were created. Various factors, such as drug, polymer, and stabilizer concentrations, were investigated for assembly in order to arrive at the most effective formulation of 5-FU-PLGNPs. PLGNPs had a drug encapsulation efficiency of 9.75 to 24.8%. The prepared nanoparticles had a spherical shape and an average size of 212.3–285 nm, as shown by TEM. The dispersion of the drug into the prepared PLGNPs was confirmed by XRPD and FTIR. The optimized nanoparticles (F225) had high encapsulation efficiency 24.8 ± 0.21%, low particles size 212.3 ± 48.2 nm with an appropriate PDI value of 0.448, and ZP of − 48.3 ± 2.7 mV. The molecular dispersion of the medication within the system was validated by thermal behavior studies (DSC). In vitro drug release from the best-selected formulations revealed a sustained release of nanoparticles, with slower release reported when lower PVA concentrations were utilized. Three 5-FU-PLGNPs formulations were tested for anticancer efficacy against cell cultures of HCT-116 (human colorectal carcinoma), MCF-7 (human breast carcinoma), and HepG2 (human hepatocellular carcinoma). The created formulations were examined for in vitro cytotoxic activity, revealing that they appeared to be promising effective anticancer formulations when compared to the positive controlled (doxorubicin).