Eptifibatide is a therapeutic cyclic peptide with poor collision-induced dissociation (CID) efficiency for multiple reaction monitoring (MRM), which limits the development of a traditional liquid chromatography-tandem mass spectrometry (LC–MS/MS) bioassay with MRM. In this study, a method combining differential mobility spectrometry (DMS) with liquid chromatography-multiple ion monitoring (LC-DMS-MIM) was developed for the quantitation of eptifibatide in rat plasma. After solid phase extraction (SPE) of 100 μL plasma on an Oasis® HLB cartridge, the analyte and I.S. (octreotide) were analyzed using a SCIEX QTRAP 6500 operated in the positive ion mode and preceded by a DMS device. The lower limit of quantitation (LLOQ) for eptifibatide was 0.5 ng/mL using only 100 μL plasma. The method was linear in the concentration range 0.5–300 ng/mL with good precision and accuracy. Compared to regulated quantitative LC–MS/MS bioanalysis of eptifibatide, the LC-DMS-MIM method effectively overcomes the sensitivity challenge in the LC-MRM method and reduces the high background noise and matrix interference in LC-MIM method without DMS. The method was successfully applied to a pharmacokinetic study involving intravenous injection of eptifibatide to Wistar rats.