Convenient, efficient and fast whole-brain delivery of transgenes presents a persistent experimental challenge in neuroscience. Recent advances demonstrate whole-brain gene delivery by retro-orbital injection of virus, but slow and sparse expression and the large injection volumes required make this approach cumbersome, especially for developmental studies. We developed a novel method for efficient gene delivery across the central nervous system in neonatal mice and rats starting as early as P1 and persisting into adulthood. The method employs transverse sinus injections of 2-4 μL of AAV9 at P0. Here, we describe how to use this method to label and/or genetically manipulate cells in the neonatal rat and mouse brain. The protocol is fast, simple, can be readily adopted by any laboratory, and utilizes the widely available AAV9 capsid. The procedure is adaptable for diverse experimental applications ranging from biochemistry, anatomical and functional mapping, gene expression, silencing, and editing.