Electrochemical determination using implantable microelectrode arrays provides a powerful tool for recording neurotransmitter concentrations across multiple spatial locations of brain tissue. In this study, nanoporous AuPt alloy nanoparticles with very rough surfaces and Nafion film were sequentially electrodeposited on Michigan-type microelectrode arrays to improve sensitivity and selectivity to dopamine (DA). The modified microelectrode arrays were characterized by scanning electron microscopy (SEM), X-ray diffractometry, cyclic voltammetry (CV), and amperometry. The results of SEM experiments indicated that the obtained AuPt alloy nanoparticles with many different sizes of pores possessed very rough surfaces and exhibited cauliflower-like shapes. During amperometric measurements, the constructed DA sensors showed a wide linear range of 0.05–12.05 μM with a high sensitivity of 73.4 ± 3.1 pA/μM. Other important features include a low detection limit of 25 nM (signal-to-noise ratio: 3), excellent selectivity over ascorbic acid (AA), and good stability. The feasibility of in vivo DA detection using the modified microelectrode arrays was verified by recording electrically evoked DA in the striatum of rats. The developed DA sensors based on microelectrode arrays provide an important tool for electrochemical detection of in vivo DA.