Tick-borne encephalitis (TBE) is a human disease caused by a flavivirus that is spread by ticks (Ixodes ricinus). In 2011 and 2012, the highest TBE incidence ever was recorded in Sweden. It has been proposed that warmer spring temperatures result in higher survival of ticks and thus high incidence of TBE. Here, analyses were done of time series of TBE for 1976-2011 in relation to the North Atlantic Oscillation (NAO), mean summer temperatures, and yearly number of harvested European hare (Lepus europeaus), roe deer (Capreolus capreolus), and red fox (Vulpes vulpes) in the County of Stockholm, the area with most TBE cases in recent years in Sweden. The results show that the winter NAO index or winter temperature has no significant effect on the variation in wildlife numbers harvested or TBE cases over time. Mean summer temperature above 12 degrees C had a slight effect, but a multivariate model revealed that only the numbers of European hare and red fox remained in the model and explained 64.4% of the variation in TBE cases. Ticks do not seem to be as sensitive to climate variations as anticipated, even though that summer temperature has increased by 2 degrees C during the time period studied here. Instead, TBE cases seem to be more dependent on host population dynamics than on climate factors.