As a chiral piperidine fungicide, fenpropidin has been widely used to control plant diseases. However, there are rare studies that have investigated fenpropidin at the enantiomer level. In this study, the single-factor analysis combined with a Box-Behnken design was used to obtain the optimal enantio-separation parameters of the fenpropidin enantiomers on ultra-performance liquid chromatography-tandem mass spectrometry. The absolute configuration of two fenpropidin enantiomers was confirmed for the first time using electron circular dichroism and optical activity. On the Lux cellulose-3 column, S-(-)-fenpropidin flowed out before R-(+)-fenpropidin. The enantio-separation mechanism was revealed by molecular docking. A modified QuEChERS method was developed for the trace determination of the fenpropidin enantiomers in seven food and environmental substrates. The average recoveries were 71.5–106.1% with the intra-day and inter-day relative standard deviations of 0.3–8.9% and 0.5–8.0%. The method was successfully verified by enantioselective dissipation of fenpropidin in soil under the field. R-(+)-fenpropidin dissipated faster than S-(-)-fenpropidin, and the half-lives were 19.8 d and 22.4 d. This study established a brand-new effective chiral analysis method for the fenpropidin enantiomers, providing a basis for accurate residue monitoring and the risk assessment of fenpropidin.