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Excessive use of alcohol can induce neurobiological and neuropathological alterations in the brain, including the hippocampus and forebrain, through changes in neurotransmitter systems, hormonal systems, and neuroimmune processes. We aimed to investigate the effects of ethanol on the expression of coding and noncoding RNAs in a brain-derived cell line exposed to ethanol. After exposing Neuro2a cells, a neuroblastoma cell line, to ethanol for 24 and 72 h, we observed cell proliferation and analyzed up- and downregulated mRNAs and long noncoding RNAs (lncRNAs) using total RNA-Seq technology. We validated the differential expression of some mRNAs and lncRNAs by RT-qPCR and analyzed the expression of <i>Cebpd</i> and <i>Rnu3a</i> through knock-down of <i>Cebpd</i>. Cell proliferation was significantly reduced in cells exposed to 100 mM ethanol for 72 h, with 1773 transcripts up- or downregulated by greater than three-fold in ethanol-treated cells compared to controls. Of these, 514 were identified as lncRNAs. Differentially expressed mRNAs and lncRNAs were mainly observed in cells exposed to ethanol for 72 h, in which <i>Atm</i> and <i>Cnr1</i> decreased, but <i>Trib3</i>, <i>Cebpd</i>, and <i>Spdef</i> increased. On the other hand, lncRNAs <i>Kcnq1ot1</i>, <i>Tug1</i>, and <i>Xist</i> were changed by ethanol, and <i>Rnu3a</i> in particular was greatly increased by chronic ethanol treatment through inhibition of <i>Cebpd</i>. Our results increase the understanding of cellular and molecular mechanisms related to coding and noncoding RNAs in an in vitro model of acute and chronic exposure to ethanol.