Two chlorogenic acids and five chlorogenic acid derivatives were simultaneously separated and purified from Stemona japonica by preparative high-performance liquid chromatography. Five of the collected compounds were over 95% pure while the other two compounds were over 90% pure. Their structures were elucidated as 3-O-feruloylquinic acid (1), 4-O-feruloylquinic acid (2), methyl 3-O-feruloylquinate (3), methyl 5-O-caffeyolquinate (4), methyl 4-O-feruloylquinate (5), ethyl 3-O-feruloylquinate (6) and the new compound ethyl 4-O-feruloylquinate (7) by UV, NMR and ESI-MS. All compounds were obtained from Stemona species for the first time, however compounds 6 and 7 are believed to be artefacts from the ethanol extraction. The anti-AIV (H5N1) activities were evaluated by Neutral Red uptake assay. Compounds 3 and 4 exerted moderate inhibitory effect against AIV (H5N1) in vitro.