Phyllanthin is a major bioactive lignan component of Phyllanthus amarus, with several known biological activities. This study dealt with the isolation and physicochemical characterization of phyllanthin. Phyllanthin was isolated from P. amarus leaves by column chromatography and purified by recrystallization to obtain phyllanthin crystals with a purity of more than 98%. UV, IR, MS, 1H NMR and 13C NMR spectra were employed to identify phyllanthin. The physicochemical properties of phyllanthin were characterized using differential scanning calorimetry, thermogravimetric analysis, X-ray diffraction, pH-solubility, ionization property and lipophilicity. The results indicated that phyllanthin crystals had the melting point and melting enthalpy range of 96.67–97.03 °C and 109.61–116.34 J/g, respectively. Three kinds of phyllanthin crystals, recrystallized by petroleum ether, absolute ethanol and 25% ethanol solution, showed only one polymorph and no polymorphic impurity. Phyllanthin in a solid state was found to undergo significant thermal decomposition above 200 °C. The compound demonstrated good stability in aqueous solution over a pH range of 1.07–10.02 for at least 4 h. The solubility of phyllanthin appeared to be pH-independent of pH range from 1.07 to 10.26. Ionization property studied by absorbance spectroscopy method was in agreement with the result of pH-solubility study, showing that phyllanthin has no pKa over a pH range of 1.12–10.02. The log Pow value of phyllanthin was found to be 3.30 ± 0.05 at pH 7.48, suggesting that phyllanthin may have good permeability through biological membranes. The findings could be useful tools for the development of stable and bioavailable oral dosage forms of phyllanthin.