Isoconazole with an asymmetrical carbon is a broad‐spectrum antimicrobial imidazole, but there is still lack of relevant report about the potential enantioselectivity in biological samples. The object of this research was to develop and validate a sensitive and effective high performance liquid chromatography‐electrospray ionization coupled with tandem mass spectrometry (HPLC‐ESI‐MS/MS) method for stereoselective separation and determination of isoconazole enantiomers in Sprague‐Dawley (SD) rat plasma and tissues. The greater enantioseparation of isoconazole enantiomers was obtained on a Chiralpak IC column with a mobile phase consisted of acetonitrile‐10 mM aqueous ammonium acetate (90:10, v/v) under the reversed‐phase mode. Subsequently, the studied compounds and internal standard (IS) were detected on a multiple reaction monitoring (MRM) mode with positive electrospray ionization source. The experimental and theoretical Electronic Circular Dichroism (ECD) spectra were employed to confirm the absolute configuration of isoconazole enantiomers. Eventually, after full method validation, the newly developed method was successfully applied to the study of enantioselectivity in plasma and tissues in SD rats. Results illustrated that the enantioselective differences in plasma were observed for the evidence that the concentrations of S‐(−)‐isoconazole were always higher than R‐(+)‐isomer. In terms of tissue distribution, liver, kidney, lung, spleen, and small intestine were the mainly distributed tissues and then followed by heart and muscle. This is the first study to reveal the stereoselective behavior of isoconazole enantiomers in vivo, which also provides reliable and valuable reference for further elucidating the enantioselective metabolisms of isoconazole enantiomers.