AbstractSR9009 and SR9011 are metabolic modulators pharmacologically targeting REV‐ERB receptors as synthetic agonists. A liquid chromatography–tandem mass spectrometry method for the detection of SR9009 and SR9011 in equine plasma was developed and validated. Plasma samples were pretreated by protein precipitation with methanol and were loaded onto an ACQUITY ultra performance liquid chromatography high‐strength silica C18 column (2.1 × 150 mm, 1.8 μm) for chromatographic separation. The mobile phase consisted of 5‐mM ammonium formate (pH 3.0) in distilled water and 0.1% formic acid in acetonitrile, and a gradient elution was used at a flow rate of 0.25 ml/min. For the mass spectrometry detection, the selected reaction monitoring mode was used with transitions of 438.2 → 124.9 for SR9009, 479.2 → 125.1 for SR9011, and 292.2 → 109.1 for the internal standard (testosterone‐d3) in the positive ionization mode. The linearity, lower limit of quantification, intra‐ and inter‐day precision, accuracy, matrix effect, recovery, and stability were evaluated. The method was found to be accurate and reproducible for the quantitation of SR9009 and SR9011. The developed method was successfully applied to plasma samples of thoroughbreds injected intramuscularly with SR9009.