Boesenbergia pandurata and its major active ingredient, panduratin A (PAN), exhibit antibacterial, anti-oxidant, anti-inflammatory, and anti-obesity effects. We explored the time course of the plasma and tissue (in the major organs, gums and skin) concentrations of PAN after oral administration of a B. pandurata extract to rats. Model-dependent analysis was used to quantify the skin distribution of PAN after systemic exposure. The PAN level peaked at 1.12 ± 0.22 μg/mL after 3 h, and then biexponentially decayed with a terminal half-life of 9 h. The mean clearance (Cl/F) was 2.33 ± 0.68 L/h/kg. The PAN levels in organs were in the following order (highest first): skin, lung, heart, gum, liver, spleen, kidney, and brain. For the first time, the time course of PAN levels in plasma and organs was investigated after oral administration of a BPE. This study helps to explain the pharmacological activities of PAN in the skin and gums. The pharmacokinetic model provided data in the plasma and skin concentrations of PAN, which are of fundamental importance to evaluate its efficacy.