Almost all human genes express multiple mRNA products (RNA isoforms), which can have different or even opposing functions. The expression of specific RNA isoforms is central to many aspects of brain development and disease, while changes in isoform expression is a key mechanism linking genetic variation with neuropsychiatric disorders. However, RNA isoforms are particularly diverse in brain and the isoforms present; their cell-type specificity; translation; and individual functions are often poorly understood. To address this, we have developed methods and software for isoform investigation, including long-read single-cell RNA-seq (LR scRNA-seq), enabling the profiling of RNA isoforms at the single cell level. We performed LR scRNA-seq on in-vitro models of human cortical development and in-vivo brain samples. LR scRNA-seq achieved high resolution identification of cell types, including subtypes of radial glial progenitors and excitatory neurons. We identified >170,000 unique isoforms, including >10,000 which were previously unknown. We discovered thousands of differentially expressed isoforms associated with synapses, axonogenesis, and neuron development. This included genes such as PKM, which showed ubiquitous gene expression but cell-type-specific isoform expression. In addition, we used proteogenomics to define translation at the isoform-level in human brain. Uncovering the expression and function of RNA isoforms will be essential for our molecular understanding of brain development and neuropsychiatric disorders, while our novel methods will be widely applicable for isoform characterisation.