Background: Informed decision making is underlined by all level of the tiers in the health system. Poor data record system coupled with under- (over)-reporting of malaria cases affects the country’s elimination activities. Thus, malaria data at health facilities and health offices are important particularly to monitor and evaluate malaria elimination progresses. This study was intended to assess overall reported malaria cases, spatiotemporal trends and factors associated in Gedeo zone, South Ethiopia, and compare malaria case reports by the health centers and health offices.Methods: Past eight years retrospective data stored in 17 health centers and 5 district health offices in Gedeo Zone were extracted. Malaria cases data at each health center with sociodemographic information, between 2012 and 2019, were included. Meteorological data were obtained from the national meteorology agency. The data were analyzed using Stata 13.Results: A total of 485,414 clinical suspects were examined for malaria during the previous 8 years at health centers. Of these suspects, 57,228 (11.79%) were confirmed malaria cases. We noted, an overall under reporting of malaria, 3,758 clinical suspects and 467 confirmed malaria cases were not captured at the health offices level. Based on the health centers records, Plasmodium falciparum (49.74%) was slightly higher (p = 0.795) than P. vivax (47.59%). The majority of cases were found in adults (≥15 years of age) that accounted for 11.47% of confirmed malaria cases (p < 0.0001). There was high spatiotemporal variation: highest cases record was during autumn (12.55%) (p < 0.0001) and, the highest (18,150, 13.17%)) and lowest (5,187 (10.44%)) malaria cases were reported from Dilla town and Yirgacheffe rural district, respectively (p = 0.0002). Monthly rainfall and minimum temperature exhibited strong positive associations with the number of confirmed malaria cases.Conclusion: A notable decline in malaria cases was observed over the eight-year period. Both P. falciparum and P. vivax co-exist; hence, control measures should continue targeting both species. The high malaria burden in urban (Dilla town) and suburban (Dilla zuria district) settings and autumn season need spatiotemporal consideration by the elimination program.