Genetic rearrangements that fuse an androgen‐regulated promoter area with a protein‐coding portion of an originally androgen‐unaffected gene are frequent in prostate cancer, with the fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2‐ERGfusion) being the most prevalent. Conventional hybridization‐ or amplification‐based methods can test for the presence of expected gene fusions, but the exploratory analysis of currently unknown fusion partners is often cost‐prohibitive. Here, we developed an innovative next‐generation sequencing (NGS)‐based approach for gene fusion analysis termed fusion sequencing via terminator‐assisted synthesis (FTAS‐seq). FTAS‐seq can be used to enrich the gene of interest while simultaneously profiling the whole spectrum of its 3′‐terminal fusion partners. Using this novel semi‐targeted RNA‐sequencing technique, we were able to identify 11 previously uncharacterizedTMPRSS2fusion partners and capture a range ofTMPRSS2‐ERGisoforms. We tested the performance of FTAS‐seq with well‐characterized prostate cancer cell lines and utilized the technique for the analysis of patient RNA samples. FTAS‐seq chemistry combined with appropriate primer panels holds great potential as a tool for biomarker discovery that can support the development of personalized cancer therapies.