In this study, an electrochemical smartphone-based aptasensor for the determination of fipronil was developed by modifying a screen-printed carbon electrode (SPCE). Fipronil is a broad-spectrum insecticide that has been widely used in various applications such as agriculture, veterinary, and household pest control. Recently, its use has raised concerns over the potential impact on the environment and human health. The absence of effective methods for this purpose poses a significant obstacle. To tackle this problem, we have developed a cutting-edge aptamer-based portable sensor capable of rapidly and conveniently detecting fipronil in situ. Considering that the detection of small molecules, such as fipronil, can be a challenging task, a competitive replacement assay was set up based on the aptamer’s preference for the free form of fipronil over the immobilized one on the electrode. The analytical performance provided by the sensor on standard solutions of a known fipronil content made it possible to estimate a limit of detection (LOD) equal to 1.07 μg kg−1 and a limit of quantification (LOQ) of 3.21 μg kg−1. Selectivity tests were conducted using atrazine as a possible interferent. The use and performance of the developed portable aptasensor was assessed on honey samples, which were simultaneously analyzed using an HPLC–MS method. This aptasensor could be an affordable and effective tool for accurately quantifying fipronil not only in honey samples but also in other food products.Graphical abstract