Fish growth and development, reproduction regulation, immune regulation, and many other life activities are regulated by long non-coding RNA (lncRNA). As a polypeptide hormone, calcitonin plays an important role in regulating calcium metabolism in vertebrates. Notably, salmon calcitonin (sCT) has the highest biological activity. To explore the effect of sCT on the expression level of lncRNAs in the skeletal tissue of teleosts, intraperitoneal injection of sCT was administered to young rainbow trout (Oncorhynchus mykiss), and their scales were collected 24 h after the injection. The lncRNA expression profile was analyzed using high-throughput sequencing technology and bioinformatics methods. A total of 847 differentially expressed lncRNAs, including 247 upregulated and 600 downregulated lncRNAs, were identified in the scales of rainbow trout administered with sCT. Six lncRNAs were randomly selected for quantitative real-time PCR (qRT-PCR) analysis; the results of which indicated that the expression pattern of these lncRNAs aligned with the RNA-Seq results. GO annotation revealed that the target genes of the aforementioned differentially expressed lncRNAs were mainly annotated in the functions of transcription regulation, transportation, signal transduction, membrane, cytoplasm, metal ion binding, and nucleotide binding. KEGG pathway enrichment analysis showed that target genes of the differentially expressed lncRNAs were significantly enriched in thiamine metabolism, inflammatory mediator regulation of TRP channels, platelet activation, glutamatergic synapse, neurotrophin signaling pathway, arrhythmogenic right ventricular cardiomyopathy (ARVC), and NF-kappa B signaling pathway. Accordingly, five lncRNAs (MSTRG.68909.2, MSTRG.39805.1, MSTRG.121429.1, MSTRG.9137.1, and MSTRG.43721.1) and their target genes might participate in the molecular regulation of O. mykiss calcium metabolism, and identification of these genes could provide a valuable dataset to elucidate the molecular regulation of bone metabolism in fish.