This study aimed to encapsulate the novel synthetic naphthoquinone ENSJ39 in liposomes, characterize them, and evaluate their in vitro cytotoxic activity in different cancer cell lines. Liposomes were obtained by the dried-lipid film hydration method, and characterizations included thermogravimetric analysis, differential scanning calorimetry, dynamic light scattering technique, and atomic force microscopy. Simulation of storage conditions, in vitro cytotoxicity by MTT, Trypan blue exclusion assay, and evaluation of morphological changes in tumor cell lines were also analyzed. Liposomes containing ENSJ39 (LE39) exhibited an average size of 31 ± 5.81 nm, zeta potential of +53.5 mV, polydispersity index of 0.24, and high encapsulation efficiency (96.58 ± 0.09%). They were thermally stable up to 250 °C and able to preserve the mass loss of the free drug. After four months of storage, they maintained excellent physical-chemical characteristics. The encapsulated drug showed less cytotoxic activity than the free drug only in HCT-116 and SNB-19 cells and caused cytoplasmic vacuolization plus an increase in the number of non-viable HCT-116 cells. ENSJ39 encapsulation method was effective in obtaining stable liposomes that presented substantial cytotoxicity activity against tumor cell lines.