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This study developed a simple, rapid, reproducible, and analytical method using liquid chromatography and electrospray ionization (ESI) with tandem mass spectrometry (LC-MS/MS) to simultaneously quantify pentoxifylline (PTX), its pharmacological active metabolites, lisofylline (PTX-M1) and 1-(3-carboxypropyl)-3,7-dimethylxanthine (PTX-M5), and donepezil (DNP) in rat plasma, using PTX-d6 and DNP-d7 as the internal standards. The LC-MS/MS procedure was performed at the ESI interface, operating in positive ionization and multiple reaction monitoring (MRM) modes; the monitoring of transitions comprised m/z 279.3 > 181.1 for PTX, m/z 281.1 > 263.1 > 160.90 for PTX-M1, m/z 267.1 > 249.0 > 220.9 for PTX-M5, m/z 380.3 > 90.9 for DNP, m/z 285.3 > 187.1 for PTX-d6 (IS1), and m/z 387.3 > 98.3 for DNP-d7 (IS2). After plasma protein precipitation (PP) with methanol, chromatographic separation was performed with an Imtakt Cadenza® CD-C18 (100 × 3 mm, 3 µm) column, using an isocratic mobile phase consisting of 0.1% formic acid in water and methanol (20:80, v/v) at a flow rate of 0.2 mL/min. The retention times of DNP, PTX-M5, PTX, and PTX-M1 were 2.24, 2.50, 2.68, and 2.72 min, respectively, with a total run time of 5 min. This method was validated over a linear concentration range of 5–8000, 10–5000, 20–15,000, and 2–500 ng mL−1 for PTX, PTX-M1, PTX-M5, and DNP, respectively, with a high correlation coefficient (r2 ≥ 0.99). The established method was fully validated in terms of selectivity, the lower limit of quantitation, precision, accuracy, recovery, matrix effect, stability, and dilution integrity according to the regulatory guidelines from the U.S. Food and Drug Administration and the Korea Ministry of Food and Drug Safety. The validated method was successfully applied to a pharmacokinetic study on the concurrent administration of DNP and PTX in rats.