A rapid, sensitive, and specific LC-MS/MS method was developed and fully validated for the detection of paeoniflorin only in rat plasma, and applied to pharmacokinetic studies, including intravenous, multi-dose oral and combined administrations with verapamil. In this study, tolbutamide was used as the internal standard, and the protein precipitation extraction method, using acetonitrile as the extraction agent, was used for the sample preparation. Subsequently, the supernatant samples were analyzed on a Phenomenex Gemini® NX-C18 column with a flow rate of 1.0 mL/min in a gradient elution procedure. In the extracted rat plasma, the method exhibited high sensitivity (LLOQ of 1.0 ng/mL) upon selecting ammonium adduct ions ([M+NH4]+) as the precursor ions and good linearity over the concentration range of 1.0–2000 ng/mL, with correlation coefficients >0.99. The intra- and inter-batch accuracy RE% values were within ±8.2%, and the precision RSD% values were ≤8.1% and ≤10.0%, respectively. The results show that the method can be successfully applied to quantitate paeoniflorin in biological samples. Additionally, paeoniflorin is subsequently confirmed to be the substrate of the P-gp transporter in vivo and in vitro for the first time, which would be necessary and beneficial to investigate the clinical safety and efficacy of PF with other drugs in the treatment of rheumatoid arthritis.