We aimed to determine the phytochemical contents of the aerial part M. neglectum aerial part (MAP) and M. neglectum bulb (MB) ethanolic extract of Muscari neglectum and to investigate their protective effects on gastric damage induced by carbon tetrachloride (CCl4) in rats. After the toxicity testing, 42 female Wistar albino rats were divided into 7 groups, Control, MAP, MB, CCl4, CCl4 + MAP, CCl4 + MB, and CCl4 + Silymarin groups. At the end of the experiment, the serum biochemical parameters, antioxidant defense enzymes, and malondialdehyde (MDA) contents in the stomach tissue were evaluated to determine the antioxidant role of the M. neglectum extracts. According to the gas chromatography–mass spectroscopy, fatty acid analysis, octadecadienoic, and 9,12,15 octadecatrienoic fatty acids were found as major fatty acids in the MAP, whereas 9,12 octadecadienoic and octadecanoic acids were the major fatty acids in the MB. According to the liquid chromatography–tandem mass spectrometry, quinic acid, fumaric acid, gentisic acid, caffeic acid, kaempferol, and apigenin were found in the MAP, while quinic acid, fumaric acid, caffeic acid, and kaempferol were found in the MB. The total phenolic and flavonoid contents in the extract were determined in the MAP and MB. The MAP and MB extracts generally caused a statistically significant decrease in the MDA content and increase in the antioxidant parameters in the stomach tissue. It was concluded that MAP and MB extracts may have antioxidant and gastric protective effects due to the phytochemical content of M. neglectum. Highlights According to LC-MS/MS results, quinic acid, fumaric acid, chemferol, apigenin, and caffeic acid were determined as major compounds in M. neglectum extracts. According to GC-MS results, octadecadienoic, octadecatrienoic, and octadecanoic methyl esters were the major fatty acids of the M. neglectum extracts. The M. neglectum extracts regulated the levels of stomach damage and biochemical parameters. The M. neglectum extracts extract might have pharmaceutical-nutritional potential.