Neuroscience, which covers the molecular mechanisms employed by the brain to cause neurological diseases and how they can be treated, remains current as the subject of high-budget investigations to develop early diagnosis and new treatment modalities with multidisciplinary approaches. For this purpose, creating the appropriate model with the correct modality and anesthesia in neurological in vivo experimental models is the most important phase to obtain accurate results and ensure animal welfare. To manage anesthesia in rodents, knowing the physiological characteristics of anesthetics and their risks will strengthen experimental procedures. Among the injectable anesthetics, ketamine, xylazine, and pentobarbital are the most frequently preferred agents for general anesthesia in short surgical procedures. Isoflurane and sevoflurane are inhaler anesthetics that are administered through a vaporizer because they are liquids. Important advantages of inhaled anesthetics, such as rapid induction and rapid withdrawal, make inhaled anesthetics stand out in neuroscience studies. In this review, the properties of frequently used anesthetic agents in rodents, their usage methods, and which model they are preferred will be discussed. For this purpose, the selection of appropriate anesthetics in animal models such as epilepsy, Alzheimer's disease, ischemia-reperfusion injury, traumatic brain injury, ischemic stroke, experimental autoimmune encephalomyelitis, and ophthalmic surgical procedures and their side effects will be reviewed.