Elucidating the mechanisms of the central nervous system necessitates the ability to precisely visualize, record, and manipulate specific neuronal populations within the living brain. Here, we report a fast and efficient technique for delivering adeno-associated virus (AAV) in neonatal pups for the robust co-expression of reporters and sensors in cortical neuronal subpopulations under different promoters and transgenic mouse lines. This approach has lower training requirements than adult AAV injections, and it enables a 40- to 50-fold increase in injection throughput per animal with high reproducibility. Pup-injected adult mice show reduced signals of neuroinflammation compared to adult-injected mice. Importantly, adult pup-injected mice have stable and high expression of multiple AAVs suitable for structure-function two-photon imaging in local cortical circuits of awake, behaving adult animals. This approach offers a fast, efficient, and robust method of introducing multiple AAVs for investigating neuronal structure and function in defined cortical neuronal populations in the living brain.