In the global incidence of peptic ulcer, with the associated rates of hospitalizations and mortality are increasing, in the United States, peptic ulcer disease affects approximately 4.6 million people annually, with an estimated 10% of the US population having evidence of a duodenal ulcer. The present research aims to find a novel treatment for ethanol induced ulcer by loading thymoquinone (TQ) on a nanostructured lipid carrier (NLC), using Compritol® 888 and coconut oil. The TQ-loaded coconut oil NLC was formulated using melt emulsification combined with a sonication method using Poloxamer 188 as a surfactant. Finally, the optimization of the formulations was performed on a three-factor, three-level Box-Behnken statistical design, with 85.63% entrapment efficiency of TQ in the optimized formulation. A biphasic release pattern of the formulation was recorded in an in vitro drug release study, where the initial burst release of the drug was observed in the first 2 h, followed by a gradual release. Later, the TQ-loaded coconut oil NLC was found to protect the gastric mucous membrane more effectively (78.95% in.; p < 0.01) in an alcohol-induced ulcer model, whereas the TQ suspension showed 30.87% inhibition (p < 0.05) of the ulcerative index, when compared with the ulcer control group. The histopathological evaluations of the stomach in ulcer-induced animals demonstrated protection potential of TQ-loaded coconut oil NLC against an alcohol-induced gastric ulcer. In a nutshell, the entrapment of TQ within the NLC was found to deliver the entrapped drug more effectively when administered through an oral route to possess a gastroprotective effect.