Coronavirus disease (COVID-19) is an infectious disease caused by a new coronavirus strain. Malaria is a parasitic disease caused by protozoan parasites of the genus Plasmodium, transmitted by mosquitoes of the genus Anopheles. The dual infection of malaria and COVID-19 is not fully understood or reported. We aimed to identify the association between malaria and COVID-19, its severity, management, and clinical outcome. This is a prospective hospital-based study conducted in isolation centers in Khartoum state during the period from October to December 2020. We used the total coverage method as a sampling technique to include participants from Khartoum isolation. We included 143 participants chosen from three centers. Data were collected from the patients and their files for those who met inclusion criteria using a questionnaire as a study tool filled out by the principal researcher. All participants in this study were COVID-19 patients diagnosed by PCR. Malaria was diagnosed in 115 patients (80.4%), and fever was the most common presenting symptom that occurred in all patients followed by fatigability in 125 (87.4%), cough in 115 (80.4), and headache in 83 (58.1%). This study found an association between malaria and COVID-19. And revealed that there is a better outcome for the patient with malaria and COVID-19 compared to those without malaria (p-value=0.036). This study revealed that there is a significant relation between COVID-19 and malaria, also it reveals that anti-malaria treatment may improve patients’ clinical outcomes. Owing to widespread COVID-19, PCR tests were considered for any patient who had malaria.