Background Extensive use of high-efficiency pyrethroid pesticides as pest-control agents lead to remarkable adsorption and release of these materials in soil and aquatic environment which could have serious adverse effects on water and food chain quality as well as human health. In this study, a molecularly imprinted polymer was synthesized and used as a selective sorbent in the sample preparation procedure in order to facilitate sensitive and quantitative exposure assessment of insecticide permethrin. Methods Molecular imprinted nanoparticles were prepared by precipitation polymerization technique using 1:4:20 mmol ratio of the template, functional monomer, and cross-linker, respectively, as well as 80 mL of chloroform as progen solvent. The obtained nanoparticles were characterized by field emission scanning electron microscopy (FESEM) and Fourier transform infrared spectrometry (FT-IR). The optimization of critical variables in the MISPE process was done using the central composite design (CCD) of the response surface methodology. Results Quadratic regressional models were developed to correlate the response and independent variables and the analysis of variance (ANOVA) verified the excellent fitting of proposed models for experimental data. Optimum conditions for the highest MISPE yield were selected as follow: sorbent mass of 7.71 mg, sample pH 5.58 and 5.68 for cis and trans-permethrin, respectively, sample flow rate of 0.6 mL/min, as well as 5 and 3.94 mL of methanol/acetic acid at the flow rate of 2 mL/min as elution solvents for cis and trans-permethrin, respectively. Under optimized conditions, the linear range was obtained 20-120 μg/L (R2 = 0.99) and the detection limits were 5.51 and 5.72 μg/L for cis and trans-permethrin, respectively. Analysis of real samples demonstrated the high extraction efficiency of designed protocol ranging from 93.01 to 97.14 with the relative standard deviation (RSD) less than 4.51%. Conclusions The satisfactory results confirmed the reliability and efficiency of the proposed method for trace analysis of permethrin isomers in biological and environmental samples.