Chromonephthea hirotai (Anthozoa; Alcyonacea; Nephtheidae) is a little-known species of soft coral that inhabits the seas around South Korea, Japan, and the wider Indo-Pacific region. In Korea, the species occurs mainly in southern coastal areas. A marked decline in the coral’s wild population has been witnessed in recent years due to climate change, and it has been identified as a species of important scientific value. However, there is little information on the genomic profile of this species, particularly regarding its stages of development, immune system, and ability to deal with environmental change. In this study, we performed a transcriptomic analysis of samples from a colony of C. hirotai. Three C. hirotai individuals were collected near Chujado, South Korea, and total RNA was extracted to construct the transcriptome assembly. The Illumina HiSeq 3000 platform was used for transcriptome sequencing, and the sequences were predicted by de novo assembly and analysis of the coding regions. Overall, 48,671 out of 129,086 unigenes were annotated in at least one public database, meaning that the overall annotation ratio of the C. hirotai assembly was 37.7%. The average length and N50 metric were 654.65 and 1118 base pairs, respectively. This study constitutes the primary documentation of the transcriptome assembly of C. hirotai in the colony phase, offering valuable insights into the genomics of this coral species. We anticipate that a framework will be developed to elucidate the mechanisms by which the azooxanthellate coral species C. hirotai responds to and develops in relation to various environmental stressors.