The common frequent precursors to head and neck squamous cell carcinoma (HNSCC) are oral dysplasias (ODs). Nonetheless, methods for prediction or prevention of the malignant transformation of OD are unreliable. Therefore, oral HNSCC is often diagnosed in the advanced stages of the disease. Abnormalities in histone acetylation in oral cancers include aberrant histone deacetylase (HDAC) expression. Therefore, HDAC inhibitors (HDACis) have potential in the treatment of HNSCC and chemoprevention for patients with high-risk OD. Valproic acid (VPA), is an anti-epileptic drug that shows HDACi activity, specifically targeting Class IIa HDACs, with efficacy against HNSCC cells; however, the molecular changes in response to VPA remain unclear. The present study aimed to determine how VPA exposure affects Class IIa HDAC mRNA expression in oral cancer cell lines (UM-SCC-10A, UM-SCC-11B, UM-SCC-12, UM-SCC-17A, HN5, PE/CA-PJ15, UM-SCC-1, BHY, PE/CA-PJ41 and UM-SCC-81B) and premalignant cells (D19, D20 and D35). Reverse transcription-quantitative PCR (RT-qPCR) revealed a trend of upregulation of HDAC4 and HDAC5, and downregulation of HDAC7 in all of the examined cells in response to 1 mM VPA exposure at different time points (6, 24 or 48 h). A total of three cell lines (precancerous D20 tongue immortal dysplastic cells, BHY oral squamous cell carcinoma cells and UM-SCC-10A laryngeal squamous cell carcinoma cells; ≥2-fold differences in HDAC expression following VPA treatment) were selected for further investigations using RT-qPCR to confirm the VPA-mediated alteration of HDAC mRNA expression. VPA-dependent epigenetic reprogramming resulted in transcriptional alterations of Class IIa HDACs in HNSCC and premalignant cells. The clinical relevance of these alterations in the pathogenesis of HNSCC must be further determined.