 A selective and sensitive electrochemical sensor has been prepared for the determination of 6-benzylaminopurine (BAP) in complex matrices. It was fabricated by thoroughly mixing multiwall carbon nanotube@SnS2 (MWNT@SnS2) with molecularly imprinted chitosan (CHIT), and then covering on the surface of glassy carbon electrode (GCE). The core/shell-structured MWNT@SnS2 dramatically improved the sensitivity of the developed sensor through providing increased binding and preconcentration onto the modified GCE, while CHIT imprinted with BAP served as the selective recognition sites. Several experimental parameters such as pH, amount of modifier, extraction time, and incubation time were optimized. Under the optimal conditions, selective detection of BAP in a linear concentration range of 0.1 nM–10 mM was performed with the detection limit of 50 pM (3Sb/S). The relative standard deviation of repeatability and reproducibility of the sensor was 1.14 and 2.42 %, respectively. Furthermore, the sensor was successfully applied to the determination of BAP in vegetable and fruit samples, indicating the molecularly imprinted polymer-based electrochemical sensing platform might provide a rapid, sensitive, and cost-effective strategy for BAP determination and related food safety analysis.