The active form of vitamin D(3), 1,25(OH)(2)D(3), exerts hierarchical control over gene expression, initially targeting transcription factors (TFs) that drive downstream responses. Here, we profile the transcriptional landscape of primary keratinocytes (HPEKp) and squamous cell carcinoma (SCC) cells in response to 1,25(OH)(2)D(3), revealing a distinct shift in regulatory targets. While TFs accounted for 9.23% of differentially expressed genes (DEGs) in keratinocytes, this proportion dropped to 4.9% with prolonged exposure. In contrast, SCC cells displayed a five-fold reduction in TFs deregulation and a concurrent enrichment of long non-coding RNAs (lncRNAs), which comprised 22.25% of DEGs after 24 h treatment, with 81% upregulated. Integrative transcriptomic and in silico analyses showed that lncRNA induction was predominantly VDR-dependent, partially RXRA-dependent, and PDIA3-independent. Notably, 90% of deregulated lncRNAs were atypical for head and neck SCC. Several of these lncRNAs exhibit potential antitumor properties and may modulate SCC cell responsiveness to interferon-gamma (IFN-γ). In conclusion, these findings suggest that in SCC cells, the regulation of lncRNA expression-rather than transcription factor modulation-may represent a mechanism of the cellular response to 1,25(OH)(2)D(3).