The number of recognized flea-borne pathogens has increased over the past decade. However, the true number of infections related to all flea-borne pathogens remains unknown. To better understand the enzootic cycle of flea-borne pathogens, fleas were sampled from small mammals trapped in central Pennsylvania. A total of 541 small mammals were trapped, with white-footed mice (Peromyscus leucopus) and southern red-backed voles (Myodes gapperi) accounting for over 94% of the captures. Only P. leucopus were positive for examined blood-borne pathogens, with 47 (18.1%) and ten (4.8%) positive for Anaplasma phagocytophilum and Babesia microti, respectively. In addition, 61 fleas were collected from small mammals and tested for pathogens. Orchopeas leucopus was the most common flea and Bartonella vinsonii subspecies arupensis, B. microti, and a Rickettsia felis-like bacterium were detected in various flea samples. To the best of our knowledge, this is the first report of B. microti DNA detected from a flea and the first report of a R. felis-like bacterium from rodent fleas in eastern North America. This study provides evidence of emerging pathogens found in fleas, but further investigation is required to resolve the ecology of flea-borne disease transmission cycles.