Babesiosis is an emerging infection in parts of New York State. From 2009 through 2016, there was a significant increase in the incidence rate of babesiosis in the Hudson Valley region of New York State (P = 0.002), an inland geographic location in which babesiosis only first emerged in 2001. A significant increase in cases was found for both the Upper Hudson Valley (UHV) region (P < 0.001) as well as for the Lower Hudson Valley region (P = 0.03). The greatest increase in the incidence rate was found for the UHV, with a 16.8-fold increase in incidence over the 8-year time period. In conclusion, babesiosis is a rapidly emerging infection in the Hudson Valley region of New York State, the geographic region now accounting for more cases than any other single geographic area in the state.