Coronavirus disease (COVID-19) is caused by a novel strain of coronavirus, while malaria is a parasitic infection triggered by Plasmodium protozoans, transmitted via Anopheles mosquitoes. The simultaneous occurrence of both malaria and COVID-19, and their interplay, remains poorly documented. This study aimed to investigate the correlation between malaria and COVID-19, focusing on the disease’s severity, treatment strategies, and clinical outcomes. The research was conducted in isolation centers in Khartoum State, from October to December 2020, as a prospective hospital-based study. Participants were selected using a total coverage sampling method from three centers in Khartoum. A total of 143 individuals participated in the study, all of whom were confirmed COVID-19 patients by PCR testing. Data were collected through patient questionnaires and medical record reviews. Malaria was diagnosed in 115 patients (80.4%), with fever being the predominant symptom in all cases, followed by fatigue in 125 (87.4%), cough in 115 (80.4%), and headache in 83 (58.1%). The findings indicate that there is a significant association between COVID-19 and malaria, such that patients with both diseases simultaneously showed better clinical outcomes compared to patients with COVID-19 alone (P-value = 0.036). The results suggest that malaria treatment may have a positive impact on the recovery of COVID-19 patients. Due to the widespread prevalence of COVID-19, PCR testing was routinely performed for any malaria-diagnosed patient.