Lyme borreliosis (LB) is the most common tick-borne disease in Germany. Mandatory notification of acute LB manifestations (erythema migrans (EM), neuroborreliosis (NB), and Lyme arthritis (LA)) was implemented in Bavaria on 1 March 2013. We aimed to describe the epidemiological situation and to identify LB risk areas and populations. Therefore, we analyzed LB cases notified from March 2013 to December 2020 and calculated incidence (cases/100,000 inhabitants) by time, place, and person. Overall, 35,458 cases were reported during the study period (EM: 96.7%; NB: 1.7%; LA: 1.8%). The average incidence was 34.3/100,000, but annual incidence varied substantially (2015: 23.2; 2020: 47.4). Marked regional differences at the district level were observed (annual average incidence range: 4–154/100,000). The Bavarian Forest and parts of Franconia were identified as high-risk regions. Additionally, high risk for LB was found in 5–9-year-old males and in 60–69-year-old females. The first group also had the highest risk of a severe disease course. We were able to identify areas and populations in Bavaria with an increased LB risk, thereby providing a basis for targeted measures to prevent LB. Since LB vaccination is currently not available, such measures should comprise (i) avoiding tick bites, (ii) removing ticks rapidly after a bite, and (iii) treating LB early/adequately.