Background Malaria is one of the main causes of death in Sudan with high prevalence among males, children under five-year and pregnant women. In 2016 near 13% of hospital admissions in Sudan were due to malaria. Community pharmacist dispensing of antimalarial drugs without prescription and malaria self-treatment may lead to the development of drugs resistance and delay disease control. Objective To assess the knowledge and practice of community pharmacists regarding malaria and its treatment. Setting Community pharmacies in Khartoum State, Sudan. Method A cross-sectional survey was carried using a structured pre-tested self-administered questionnaire for the pharmacists in charge of 320 randomly selected community pharmacies. Main outcome measures The community pharmacists'knowledge and practices regarding malaria and antimalarials dispensing. Results A total of 293 pharmacists participated in the study giving a response rate of 91.5%. About 92.2% of the respondents were from the age of 20-39 years and 63.8% had less than 5 years of experience. Community pharmacists showed inadequate knowledge regarding malaria and its treatment. In addition to that, they were dispensing antimalarials without prescriptions. The community pharmacists reported many barriers to their effective contribution in malaria prevention and treatment such as lack of knowledge, lack of time and lack of training. Conclusion Inadequate knowledge and irrational antimalarials dispensing practices were reported among the community pharmacists in Khartoum State. Although training was a significant predictor of pharmacists' knowledge regarding malaria and its treatment, health authorities were not providing regular training for the practicing pharmacists.