Presynaptic active zones (AZs) form during synaptogenesis and are critical for ensuring precise synaptic transmission. Although much is known about the development of AZs at the neuromuscular junction, their assembly in the Drosophila central nervous system (CNS) remains incompletely understood. Here, we demonstrate the mushroom body α/β Kenyon cells in young adults in which new AZs are continuously formed, as a novel system to dissect the sequential AZ assembly in the CNS. With this system we show proof of principle using a tagged allele of the cell-adhesion molecule Neurexin-1 to investigate the structural maturation of synapses in the fly brain.