This study was carried out to analyze spatial and temporal incidence characteristics of scrub typhus and predict the future incidence of scrub typhus since the incidences of scrub typhus have been rapidly increased among vector-borne diseases. A maximum entropy (MaxEnt) ecological model was implemented to predict spatial distribution and incidence rate of scrub typhus using spatial data sets on environmental and social variables. Additionally, relationships between the incidence of scrub typhus and critical spatial data were analyzed. Elevation and temperature were analyzed as dominant spatial factors which influenced the growth environment of Leptotrombidium scutellare (L. scutellare) which is the primary vector of scrub typhus. A temporal number of diseases by scrub typhus was predicted by a deep neural network (DNN). The model considered the time-lagged effect of scrub typhus. The DNN-based prediction model showed that temperature, precipitation, and humidity in summer had significant influence factors on the activity of L. scutellare and the number of diseases at fall. Moreover, the DNN-based prediction model had superior performance compared to a conventional statistical prediction model. Finally, the spatial and temporal models were used under climate change scenario. The future characteristics of scrub typhus showed that the maximum incidence rate would increase by 8%, areas of the high potential of incidence rate would increase by 9%, and disease occurrence duration would expand by 2 months. The results would contribute to the disease management and prediction for the health of residents in terms of public health.