PurposeMalaria has been one of a major infectious parasitic disease in Nepal. Although the number of cases is gradually getting declined since last decade. Therefore, study aims to identify the trends and spatial patterns of malaria among 25 risk districts of Nepal.Materials and MethodsThis study utilized the secondary data of malaria cases from the annual reports (2001–2017) of Department of Health Services, Ministry of Health and Population of Nepal. Linear regression of log-transformed incidence rates model was used for assessing variation of malaria cases for year and districts.ResultsThere was evidence of decrease in the trend of malaria (2001–2009); however, the upward trend was revealed in 2010, after that, it starts to decline and again in 2017, it started to grow up. The malaria cases were marked variations by location with higher rates occurring in Dadeldhura, Kanchanpur, Kailali, Bardiya, and Jhapa districts, respectively.ConclusionIn this regards, malaria cases are still causing the threat in the Terai district of Nepal; however, there were fluctuating patterns of disease noted during the study periods.