Mangiferin is an important xanthone compound presenting various biological activities. The objective of this study was to develop, characterize physicochemical properties, and evaluate the anti-topoisomerase activity of poly(lactic-co-glycolic acid) (PLGA) nanoparticles containing mangiferin. The nanoparticles were developed by the emulsion solvent evaporation method and the optimal formulation was obtained with a response surface methodology (RSM); this formulation showed a mean size of 176.7 ± 1.021 nm with a 0.153 polydispersibility index (PDI) value, and mangiferin encapsulation efficiency was about 55%. The optimal conditions (6000 rpm, 10 min, and 300 μg of mangiferin) obtained 77% and the highest entrapment efficiency (97%). The in vitro release profile demonstrated a gradual release of mangiferin from 15 to 180 min in acidic conditions (pH 1.5). The fingerprint showed a modification in the maximum absorption wavelength of both the polymer and the mangiferin. Results of anti-toposiomerase assay showed that the optimal formulation (MG4, 25 µg/mL) had antiproliferative activity. High concentrations (2500 µg/mL) of MG4 showed non-in vitro cytotoxic effect on BEAS 2B and HEPG2. Finally, this study showed an encapsulation process with in vitro gastric digestion resistance (1.5 h) and without interfering with the metabolism of healthy cells and their biological activity.