The main objective of this study was to investigate possible application of citron (Citrus junos Sieb. ex TANAKA) seeds, which are massively produced as by-products during citron tea process, into functional food materials. First of all, citron seeds were germinated and produced citron shoots were examined for their functional properties. When contents of flavonoids in citron seeds and their germinated shoots were compared, naringenin, neohesperitin, and hesperitin were remarkably increased in shoots after germination while naringin and didymin were decreased. Concentrations of limonin and nomilin were decreased by germination otherwise their unidentified derivatives were newly formed. A methanol extract of citron shoot had lower $IC_{50}$ values [0.13 and 0.07 mg/mL for 2,2-diphenyl-1-picryl-hydrazyl (DPPH) and ABTS, respectively] than citron seed extract in radical scavenging activities. Addition of 500 mg/mL of citron shoot extract suppressed fat accumulation in 3T3-L1 adipocytes by 36.9%. Oral administration of olive oil along with citron shoot extract (33 mg/kg body weight) to Sprague Dawley rats effectively inhibited absorption of lipid into a body by decreasing blood triglyceride levels from 105.1 to 74.9 mg/dL 2 hr after olive oil administration. According to these results, citron shoot extract as a rich source of flavonoids can be utilized for functional food ingredients with effective antioxidant and anti-adipogenic properties.