RNA-binding proteins (RBPs) regulate genetic diversity, but the degree to which they do so in individual cell types in vivo is unknown. We developed NOVA2 cTag-crosslinking and immunoprecipitation (CLIP) to generate functional RBP-RNA maps from different neuronal populations in the mouse brain. Combining cell type datasets from Nova2-cTag and Nova2 conditional knockout mice revealed differential NOVA2 regulatory actions on alternative splicing (AS) on the same transcripts expressed in different neurons. This includes functional differences in transcripts expressed in cortical and cerebellar excitatory versus inhibitory neurons, where we find NOVA2 is required for, respectively, development of laminar structure, motor coordination, and synapse formation. We also find that NOVA2-regulated AS is coupled to NOVA2 regulation of intron retention in hundreds of transcripts, which can sequester the trans-acting splicing factor PTBP2. In summary, cTag-CLIP complements single-cell RNA sequencing (RNA-seq) studies by providing a means for understanding RNA regulation of functional cell diversity. Display omitted •cTag-CLIP provides a strategy to study cell-specific RNA regulation in vivo•NOVA2 controls unique RNA splicing programs in inhibitory and excitatory neurons•NOVA2 cTag-CLIP reveals a new mechanism of cell-specific AS regulation•NOVA2 regulates intron retention as a cis-acting scaffold for AS factor PTBP2 cTag-CLIP provides a next-generation strategy to profile functional protein:RNA interactions at cell-specific resolution in vivo. Saito et al. show that differential NOVA2 regulatory actions on alternative splicing coupled to intron removal in different neurons.