Background Malaria is one of the main public health challenges in Ethiopia that hinder the productivity and development of the country. In 2018, Ethiopia is on track to minimize the incidence of malaria by 40% as per its 2020 malaria reduction strategy. Currently, Ethiopia is working to eliminate malaria in 2030 by extending the 2020 strategy. Hence, this study aimed to analyze the trend of malaria prevalence in Wolkite health center, Gurage zone, Southern Central Ethiopia from 2015 to 2018. Methods A retrospective study was conducted to determine the prevalence of malaria by reviewing the malaria registration laboratory logbook at Wolkite health center from 2015 to 2018. For all patients, blood films were done for the detection of malaria cases. All the socio-demographic data, year, month and malaria data were collected using a predesigned data collection sheet from January to March, 2019. Results From a 121,230 clinically malaria suspected patients, the overall prevalence of microscopically confirmed cases were 8.56% (n = 10,379/121,230). Plasmodium vivax was the most predominant species accounted for 69.7% (n = 7237/10,379) followed by Plasmodium falciparum 29.3% (n = 3044/10,379). Age group > 15 years old were more affected by malaria accounting 54% (n = 5609/10,379) and malaria cases regarding sex were proportional (51.1% of males and 48.3% of female). Among the catchment areas, a higher number of malaria prevalence was recorded in the Wolkite town 66.2% (n = 0.6538/10,379). Higher malaria cases were shown in the season of Spring 29.8% (n = 3096/10,379) while lower cases 20.4% (n = 2123/10,379) were seen in the Winter season. Conclusion The prevalence of malaria in Wolkite health center showed a consistent downward trend from the year of 2015–2018. Importantly, the higher prevalence of P. vivax seems overlooked in the study area. Therefore, malaria prevention and control strategy should be reinforced to reduce the prevalence of malaria in the study area.