The basophil histamine release test (HRT) is an important in vitro diagnostic assay to evaluate immunoglobin E (IgE)-mediated allergic responses. In this study, a bioanalytical LC–MS/MS method was developed and validated to quantify histamine in the leukocyte suspension from human peripheral blood. The method used pre-column derivatization with phenylisothiocyanate (PITC) and the resulting phenylthiocarbamyl (PTC) histamine was analyzed by positive-ion electrospray ionization using the multiple reaction monitoring mode. Chromatographic separation was achieved using an Imtakt-HT C18 column (2.1 mm × 50 mm, 3.0 μm), with a flow rate of 0.35 mL/min, 2 μL injection, and gradient elution with a mixture of acetonitrile-2 mM ammonium acetate buffer (both containing 0.1% formic acid). The total runtime of the method was 3.0 min including equilibration time. The method had a lower limit of detection of 0.1 ng/mL, and the quantifiable range was 0.1–100 ng/mL in the leukocyte suspension. The intra-day and inter-day precision and accuracy results were within the acceptable limits. It was established that histamine quantification should be performed within 2 h of preparing the leukocyte suspension, and freezing and thawing should be avoided. This method was successfully applied to the diagnosis and evaluation of the pathophysiologic mechanism of respiratory or cutaneous allergic diseases.