Background: In Gabon, a new national malaria control policy was implemented in 2003. It resulted in a decrease in the number of malaria cases in the country. In March 2020, the disruption of routine health services due to the COVID-19 pandemic has led to an increase in cases and deaths due to malaria. However, in Franceville, south-east Gabon, no data on malaria cases recorded before, during and after the COVID-19 epidemic has been published. Thus, the objective of this study was to determine the epidemiological characteristics of malaria in Franceville from 2019 to 2021. Methods: A retrospectively study of malaria cases was performed at the Hopital de l'Amitie Sino-Gabonaise (HASG). Information regarding age, gender, malaria diagnosis by microscopy and hematology cell count were collected from laboratory registers from June 2019 to December 2021. Malaria data were analyzed and correlated with seasonal variations. Results: The data of 12,695 febrile patients were collected from the laboratory registers of the HASG, among which 4252 (33.5%) patients were found positive for malaria. The malaria prevalence was 37.5% in 2020 year. This prevalence was highest compared to the 2019 (29.6%) and 2021 (31.5%) year (p < 0.001). During the short rainy season (October to December), a large increase in malaria cases was observed all three year, from 2019 to 2021 (p > 0.05). Conclusion: The prevalence of malaria in Franceville was very high during COVID-19 pandemic. It is therefore necessary to strengthen existing interventions and implement more effective interventions.