Fargesin, a tetrahydrofurofuranoid lignan isolated from Flos Magnoliae, shows anti-inflammatory, anti-oxidative, anti-allergic, and anti-hypertensive activities. To evaluate the pharmacokinetics of fargesin in mice, a sensitive, simple, and selective liquid chromatography-high resolution mass spectrometric method using electrospray ionization and parallel reaction monitoring mode was developed and validated for the quantification of fargesin in mouse plasma. Protein precipitation of 6 µL mouse plasma with methanol was used as sample clean-up procedure. The standard curve was linear over the range of 0.2–500 ng/mL in mouse plasma with the lower limit of quantification level at 0.2 ng/mL. The intra- and inter-day coefficient variations and accuracies for fargesin at four quality control concentrations including were 3.6-11.3% and 90.0-106.6%, respectively. Intra-venously injected fargesin disappeared rapidly from the plasma with high clearance values (53.2-55.5 mL/min/kg) at 1, 2, and 4 mg/kg doses. Absolute bioavailability of fargesin was 4.1-9.6% after oral administration of fargesin at doses of 1, 2, and 4 mg/kg to mice.