Background: Methotrexate (MTX) is an anti-metabolite most commonly used in chemotherapy and immunosuppressant in auto-immune diseases. It is one of the major choices to treat various types of cancers. Thymoquinone (TQ) is the principal component of Nigella sativa (N. Sativa). It has prominent therapeutic actions as it possesses antiapoptotic, antioxidant, antimicrobial, and, hepatoprotective activities. Objective: This study aimed to clarify the possible effect of TQ on the histological changes of the cerebellar cortex of MTX -treated adult male albino rats. In addition, to assess the restoration of the normal histological structure after cessation of MTX. Materials and Methods: Thirty six adult healthy male albino rats were divided into four groups; group I (Control group), group II (MTX group) received (0.5 mg/kg BW) MTX intraperitoneally (i.p.) twice a week for four weeks. Group III (MTX and TQ group) received MTX intraperitoneally similar to (group II) in concomitant with TQ orally at a dose of (10 mg/kg BW) dissolving in (1ml) distilled water daily for four weeks, and group IV (recovery group) received MTX intraperitoneally similar to (group II) then left without treatment for 15 days. At the end of the experiment, all rats were anesthetized and cerebellar specimens were obtained and processed for light and transmission electron microscope examination. Morphometric and statistical analyses were also performed. Results: During the experiment, MTX group showed gradual deterioration of the motor activities and a statistically significant decrease in the body weight, Microscopic examination displayed shrunken Purkinje cells with darkly stained pyknotic nuclei. Cresyl fast violet-stained cerebellar sections showed ill-defined purple Nissl granules in the perikarya of Purkinje cells and other neurons.Immunohistochemical-stained sections for GFAP showed a strong positive reaction in the processes of astrocytes, weak positive reaction for Bcl-2 in neuronal cytoplasm. MTX and TQ-treated groups showed no deterioration in their motor activities. Most Purkinje cells had a pyriform shape, vesicular nuclei, and basophilic cytoplasm. Few Purkinje cells appeared irregular and darkly stained. Signs of degeneration were still present in the cerebellar cortex of the recovery group. Conclusion: The cerebella of MTX- treated albino rats showed evident structural alterations seen by light and electron microscopes and also marked changes in the immunohistochemical reactions indicating its neurotoxicity. Co-administration of TQ attenuated these changes more than cessation of MTX. This indicates TQ neuroprotective effect which can be considered clinically.