We developed an electrochemical paper-based device (ePAD) for the online separation and simultaneous determination of structurally similar carbofuran (CBF) and carbaryl (CBR). Our device combined paper chromatography and an electrochemical sensor as a single system for increasing the selectivity to simultaneous detection of the two pesticides. During the simultaneous detection of CBF and CBR, the separation of the two carbamate compounds depends on the differences between the movements of the substances on the chromatographic paper in the moving phase flow. The isolated pesticides were electrochemically measured using an amperometric method. Under optimal conditions, which include the effect of the mobile phase, separation channel, and the applied potential, the proposed device provides a linear range for the simultaneous determination of CBF and CBR from 0.1 to 2.0 and 0.5–7.5 mg L−1, with the limits of detection at 0.06 and 0.40 mg L−1, respectively. Furthermore, we successfully used the developed device to determine CBF and CBR in water, cucumber, and cabbage samples. The obtained results correspond to results obtained from a standard method. This developed ePAD is low-cost and uses a low sample volume (2 µL). Moreover, it is disposable, portable, and a promising tool for the on-site quantification of pesticides in actual samples.