To explore useful natural compounds from indigenous medicinal plants, the cytotoxic properties from a methanolic extract of Boehmeria sieboldiana leaves against human cancer cell lines were isolated in the present study. After purification of the extract, seco-dehydroantofine B (1) together with two known phenanthroindolizine alkaloids, seco-dehydroantofine A (2) and septicine (3), were isolated. The structure of seco-dehydroantofine B was elucidated by performing comprehensive one- and two-dimensional nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The cytotoxicity of these compounds against five human tumor cell lines was evaluated. Compound 3 exhibited anti-tumor activity at IC50 values of 50.0, 66.9, 50.0, and 153.7 µM against MKN1, SAS, HL-60, and THP-1 cells, respectively.