Neuropsychiatric disorders are a spectrum of complex and highly debilitating conditions. Genetic risk plays an important part in who develops neuropsychiatric disorders and many risk genes are being identified, but the underlying mechanisms are poorly understood. In the recent years, there has been increasing evidence suggesting a role for alternate splicing and lncRNAs in these disorders. However, sequencing-based validation of these events has been limited by the scope of short read sequencing and/or the low expression levels of lncRNAs. This study aimed to compare the performance of targeted short and long-read sequencing (CaptureSeq) for the quantification and identification of risk gene isoforms and lncRNAs. We performed short-read (SR), capture short-read (CapSR), capture long-read (CapLR) and capture long-read with preferential selection of reads >1.5 kb (CapLR-FracCap) sequencing on three regions of postmortem brain. CapLR-FracCap sequencing identified and quantified the largest number (47) of captured risk genes and transcript isoforms (178), following by CapLR. Long-read methods identified more gene and transcripts despite the ~20x greater number of reads sequenced with short-read methods. The two long-read techniques were also extremely effective in identifying novel transcriptomic features missed by the two short-read methods such as novel gene isoforms, novel exons in the captured genes and putative novel genes in intergenic regions. These results indicate the potential of long-read capture sequencing for effective quantification of the transcriptome and detection of novel isoforms and transcripts.