We present an electrochemical, microfluidic system with a working electrode based on an ordered 3D array of pencil leads. The electrode array was integrated into a plexiglass/PDMS channel. We tested the setup using a simple redox probe and compared the results with computer simulations. As a proof of concept application of the device we showed that the setup can be used for determination of dopamine concentration in physiological pH and ultrasensitive, although only qualitative, detection of p-nitrophenol with a limit of detection below 1 nmol L−1. The observed limit of detection for p-nitrophenol is not only much lower than achieved with similar methods but also sufficient for evaluation of exposure to pesticides such as methyl parathion through urinalysis. This low cost setup can be fabricated without the need for clean room facilities and in the future, due to the ordered structure of the electrode could be used to better understand the process of electroanalysis and electrode functionalization. To the best of our knowledge it is the first application of pencil leads as 3D electrochemical sensor in a microfluidic channel.