A rapid, simple and sensitive chiral HPLC method was developed and validated for quantification of biologically important alkaloids namely evodiamine enantiomers and rutaecarpine in Evodiae fructus using diphenhydramine as the internal standard (IS). Chromatographic separations were performed on a Chiralpak AD-H® column (250 mm × 4.6 mm i.d., 5 μm) with elution of n-hexane–2-propanol–ethanol (70:20:10, v/v/v) in a flow rate of 0.7 ml/min and at λmax 225 nm. To identify the order of elution, small quantities of the each evodiamine enantiomer were isolated by semi preparative HPLC method. Extraction samples were prepared by a simple solid phase extraction (SPE) method. All calibration curves showed good linearity (r2 ≥ 0.999) within the test ranges. The LOD and LOQ were lower than 0.05 and 0.1 μg/ml, respectively. The RSDs of intra- and interday for relative peak areas of three analytes to IS were less than 3.2 and 2.5%, respectively, and the recoveries were 98.0–103.7%. The validated method was successfully applied to the quantitative analysis of three constituents in 13 batches of samples collected from market. The results showed that S-(+)-evodiamine was the main component while R-(−)-evodiamine was present in low concentration. This study provides a qualitative and quantitative method for analysis of evodiamine enantiomers and rutaecarpine, and should be extendable to pharmacological and toxicological studies of the individual evodiamine enantiomers.