The composition of volatile oils of the leaf and stem of Farfugium japonicum (L.) Kitamura were prepared by supercritical fluid extraction (SFE)-CO2. A total 47 and 40 compounds were identified by GC/MS analysis, respectively, and only 13 compounds coexisted. The main constituent types in the leaf oil included alcohols (34.1%), hydrocarbons (24.1%), terpenoids (16.2%), benzenes (7.5%), and fatty acids (4.9%). In the stem oil, the constituent types chiefly included benzenes (18.8%), ketones (13.9%), terpenoids (17.0%), fatty acids (8.8%), phenolics (8.7%), steroids (8.6%), hydrocarbons (8.0%), and esters (5.7%). The predominant volatile compounds in the stem were 2-(1-cyclopent-1-enyl-1-methylethyl) cyclopentanone (11.7%), 1,2,3,4,5,6,7,8-octahydro- 9,10-dimethyl-anthracene (8.4%), 5-heptylresorcinol (6.5%), and α-sitosterol (5.2%). Those in the leaf mainly included (E)-3-hexen-1-ol (13.7%) and (Z)-3-hexen-1-ol (14.0%). This demonstrated a significant difference in the composition of both oils. Further study showed that stem oils demonstrated the highest DPPH (1,1-diphenyl-2-pinylhydrazyl) and ·OH free radical scavenging capacities at IC50 values of 9.22 and 0.90 mg/mL, respectively. In addition, they demonstrated the strongest antibacterial capacity against the Gram-positive bacteria methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) at a minimum inhibitory concentration (MIC) of 0.16 mg/mL. This could be due to the SFE-CO2 extraction and the high accumulation of benzenes, terpenoids, and phenolics in the stem. In particular, the monoterpenes presented in terpenoids could play a special role in these findings.