Objective: The study aimed to determine the prevalence of malaria in Halaba special district, Southern Ethiopia, from 2013 to 2017.

Results: Of a total 583,668 malaria suspected cases examined during the study period, 55,252 (9.5%) were microscopically confirmed to be positive for malaria, at the rate of 27,712 (50.2%) females and 27,540 (49.8%) males (P = 0.95). The highest prevalence of 8454 (15.3%) malaria cases were observed in Halaba health center, followed by Halaba district hospital, at 7290 (13.2%), while the lowest cases, 1765 (3.2%), were confirmed in Wejago health center. The highest prevalence of malaria, 25,716 (46.5%), was registered among the age group ≥ 15 year old (P = 0.006). Plasmodium vivax and Plasmodium falciparum were the two major malaria parasites detected in this study, with the prevalence of 33,855 (62.3%) and 21,397 (38.7%), respectively (P = 0.0001). The detected high prevalence of P. vivax in this study may clearly indicate that more attention has been given to control P. falciparum strains in the study area. This may be a great challenge for the achievement of malaria elimination goals. Therefore, all concerned bodies should act collaboratively to combat the high prevalence of P. vivax from the study district.