The inclusion behavior of sulfobutylether-${eta}$-cyclodextrin (SBE-${eta}$-CD) with perphenazine (PPH) was first studied by flow injection (FI)-chemiluminescence (CL) analysis with proposed $lg[(I_0-I_s)/I_s]=lgK_{P-CD}+nlg[C_{PPH}]$ model and molecular docking. Results showed that a 1:1 complex of SBE-${eta}$-CD/PPH could online form, with the formation constant $K_{P-CD}$ of $2.57{ imes}10^7Lmol^{-1}$ at 298 K. The thermodynamic parameters showed that the inclusion behavior of SBE-${eta}$-CD/PPH was a spontaneous process by hydrophobic interaction. The molecular docking results revealed PPH entered into the larger cavity of SBE-${eta}$-CD with two hydrogen bonds. Based on the linear relationship of the decrement of luminol/SBE-${eta}$-CD/PPH CL intensity against the logarithm of PPH concentration ranging from 0.03 to 30.0 ng $mL^{-1}$, the present FI-CL analysis using luminol/SBE-${eta}$-CD/PPH system was successfully applied to PPH determination in biological fluids and tablets with recoveries from 94.5 to 105.6% and RSDs less than 2.6% (n = 5).