HYNIC-3PRGD2 is used to prepare a new 99mTc-radiolabeled tracer. HYNIC-3PRGD2, which has a high binding affinity for the integrin αvβ3due to its special structure, has become a promising tumor imaging agent for diagnosis and monitor of the clinical response to therapeutic effects of anti-tumor agents. Here, we developed and validated a method for determination of HYNIC-3PRGD2 concentration in rat plasma using ultra-high performance liquid chromatography-tandem mass spectrometry system. Following sample extraction by methanol precipitation, satisfactory separation through chromatography was achieved on an hydrophilic reverse-phase C18 column AQ (2.1 mm × 100 mm, 2.7 μm) at a flow rate of 0.2 mL·min-1 with an gradient elution using mobile phase consisting of ultrapure water and acetonitrile fortified with 0.1% formic acid respectively. The calibration curve was developed over a linear range of 3.125-100 ng·mL-1 with the lower limit of quantification of 3.125 ng·mL-1. The HYNIC-3PRGD2 and its internal standard c(RGDfK)(RK5) were detected and quantified with the multiple reaction monitoring (MRM) mode on a triple-quadrupole tandem mass spectrometer. This method was successfully validated and applied for pharmacokinetic evaluation of HYNIC-3PRGD2 during pre-clinical experiments.