Bisphosphonates and myo‐inositol trispyrophosphate (ITPP) are two classes of difficult‐to‐detect polar drugs that are prohibited under the rules of racing. ITPP is a drug capable of increasing the amount of oxygen in hypoxic tissues, and studies have shown that administration of ITPP increases the maximal exercise capacity in mice. The properties of ITPP make it an ideal candidate as a doping agent to enhance performance in racehorses. In recent years, ITPP had indeed been detected in racehorses and confiscated items. As for bisphosphonates, it is especially critical to control their use as since February 2019, the International Agreement on Breeding, Racing and Wagering (IABRW) by the International Federation of Horseracing Authorities (IFHA) had identified specific conditions on which bisphosphonates should not be administered to a racehorse. A recent review of literature shows that there is yet a simultaneous screening method for detecting ITPP and bisphosphonates in equine samples. This paper describes an efficient ion chromatography high‐resolution mass spectrometry (IC‐HRMS) method for the simultaneous detection of ITPP and 10 bisphosphonates at sub‐parts‐per‐billion (ppb) to low‐ppb levels in equine plasma after solid‐phase extraction (SPE) and its application to an administration study of clodronic acid in horses.