Abstract Background Oral mucositis is a frequent side effect of anticancer treatments. It impairs the patient’s quality of life, aggravate clinical condition, increase the risk of infection and can delay anticancer treatment. Health care workers at the NIBD and BMT Karachi, Pakistan emphasize on oral hygiene to prevent such complications for the patients. Proper oral hygiene protocol can reduce the risk of oral ulcers. In this study we have done the evaluation of oral hygiene. At NIBD and BMT among pediatric population are advice to brush their teeth twice a day, use pyodine/ Chlorhexidine 0.2% mouth wash thrice a day followed by application of anti-fungal jell. Methods A cross-sectional survey was conducted from date 8/5/2020 to 11/5/2020 at children hospital. 73 admitted patients were the study using convenient sampling, team approached eligible patients and informed consent was obtained from parents. A standardized questionnaire was then administered in Urdu (Pakistan’s national language). Results 11% of patients reported that they frequently or always suffered from oral ulcer and use mouth washes for gargles; however 79.5% reported that they rarely or never suffered from oral ulcer and use mouth washes. In contrast, 9.6% patients reported that they rarely or never suffered from oral ulcer and do not use mouth washes, whereas none of the patients who reported that they do not use mouth washes for gargles had suffered from oral ulcer frequently or all the time. 2.7% of the patients experienced oral ulcer frequently or always and brush once in a day, 6.8% experienced oral ulcer frequently or always and brush twice or more in a day and 1.4% don’t brush and suffered from oral ulcer frequently or always. Conversely, 27.4% never or rarely had oral ulcer and brush once in a day, 54.8% never or rarely had oral ulcer and brush twice or more in a day and 6.8% don’t brush and had never or rarely experienced oral ulcer Conclusion The use of proper oral hygiene protocol can decrease the risk of chemotherapy induced mucositis. Majority of the patients at NIBD 02 + 103 understand the importance of oral hygiene after their doctor’s Furthermore oral hygiene can decrease levels of oral mucositis and eventually decrease inpatient admissions, delays in treatments and improving the quality of life.