A rapid and sensitive method for determining usnic acid of Lethariella cladonioides in rat was established using high performance liquid chromatography (HPLC) quadrupole time-of-flight (QTOF) tandem mass (MS/MS). Rat plasma was pretreated by mixture of acetonitrile and chloroform to precipitate plasma proteins. Chromatographic separation was achieved on a column (50 × 2.1 mm, 5 μm) with a mobile phase consisting of water (containing 5 × 10−3 M ammonium formate, pH was adjusted to 3.0 with formic acid) and acetonitrile (20:80, v/v) at a flow rate of 0.3 mL/min. A tandem mass spectrometric detection with an electrospray ionization (ESI) interface was conducted via collision induced dissociation (CID) under negative ionization mode. The MS/MS transitions monitored were m/z 343.0448 → m/z 313.2017 for usnic acid and m/z 153.1024 → m/z 136.2136 for protocatechuic acid (internal standard). The linear range was calculated to be 2.0-160.0 ng/mL with a detection limit of 3.0 pg/mL. The inter- and intra-day accuracy and precision were within ± 7.0%. Pharmacokinetic study showed that the apartment of usnic acid in vivo confirmed to be a two compartment open model. The method was fully valid and will probably be an alternative for pharmacokinetic study of usnic acid.