Introduction: Methotrexate is antimetabolite drug, that was used in the management of many malignant conditions. The main mechanism of MTX cytotoxicity involves a reduction in the effectiveness of the antioxidant enzyme defense system. So, antioxidants as L-carnitine may protect against oxidative stress induced cell damage by MTX. Aim: To evaluate the possible prophylactic and therapeutic effect of L-carnitine on the submandibular salivary gland of methotrexate treated rats, histological and immunohistochemical examination to localize caspase-3 and BCL-2 were carried out. Materials and Methods: Fifty male Wistar rats with an average of 150 -200 grams were divided into five groups, 10 rats for each group as following: Group 1: rats received no treatment. Group 2: rats received a single intraperitoneal injection of 20mg/kg MTX on day 5. Group 3: rats received: L-carnitine as intraperitoneal injection 500mg/kg per day & MTX as single intraperitoneal injection 20 mg/kg on day 5. Group 4: rats received 20 mg /kg of MTX as single intraperitoneal injection on day 5. & L-carnitine 500 mg / kg was given as treatment from day 5 till day 10. Group 5: rats received L-carnitine as intraperitoneal injection 500mg/kg per day. Subsequent to the experiment rats were euthanized and submandibular gland specimens were collected for histological and immunohistochemical examinations. All data was collected and statistically analyzed by the computer program SPSS software for windows version 26.0. Results: L-carnitine has a protective role against methotrexate cytotoxic effects and its usage as a prophylactic is more effective than its usage as a therapeutic drug. Conclusion: L-carnitine has a protective role against methotrexate cytotoxic effects and its use as a prophylactic drug was more effective than its use as a therapeutic one.