Chlorogenic acid (CGA) is a polyphenol derivative that widely exists in higher plants like fruits, vegetables, black teas, and some traditional Chinese medicines. In this work, we have proposed a sensitive and selective electrochemical sensor for detection of CGA. The sensor was based on a glassy carbon electrode (GCE) modified with a functional platform by grafting vinyltrimethoxysilane (VTMS) in multi-walled carbon nanotubes (MWCNTs) and covered by a molecularly imprinted siloxane (MIS) film prepared using the sol-gel process. The VTMS was grafted onto the surface of the MWCNTs via in situ free radical polymerization. The MIS was obtained from the acid-catalyzed hydrolysis/condensation of a solution consisting of tetraethoxysilane (TEOS), phenyltriethoxysilane (PTEOS), (3-aminopropyl)trimethoxysilane (APTMS), and CGA as a template molecule. The modification procedure was evaluated by differential pulse voltammetry (DPV) and scanning electron microscopy (SEM). Under optimized operational conditions, a linear response was obtained covering a concentration ranging from 0.08μmolL−1 to 500μmolL−1 with a detection limit (LOD) of 0.032μmolL−1. The proposed sensor was applied to CGA determination in coffee, tomato, and apple samples with recoveries ranging from 99.3% to 108.6%, showing a promising potential application in food samples. Additionally, the imprinted sensor showed a significantly higher affinity for target CGA than the non-imprinted siloxane (NIS) sensor.