Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16^th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom—a skeleton from the Great Chesterford cemetery with a calibrated age of 415–545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide. Many controversies surround leprosy, which is one of the oldest recorded diseases of humankind. The origin and past spread of its main causative agent, Mycobacterium leprae, remain unknown although many attempts have been made to reconstruct its past from historical and archeological sources. Analysis of ancient M. leprae genomes reconstructed from archaeological remains can contribute greatly to reconstructing the origin and evolution of this pathogen. With a new set of ancient M. leprae genomes from Europe, we traced back a so far unrecognized past diversity, which places Europe as a key region for the early spread and worldwide dissemination of leprosy. Our results hint to the potential dynamic changes in the prevalence of different M. leprae strains in Europe during Antiquity, and highlight the need to study ancient pathogen genomes in order to better understand our past.