Animal relocation programs seek to balance the animal population and resources between source and destination communities to promote positive outcomes, though little objective evidence has been reported on their physical and behavioral implications. The objective of the current report is to describe the incidence and predictors of canine parvovirus (CPV) diagnoses in 8- to 19-week-old puppies reported by destination shelters participating in a large scale, long-distance, structured animal relocation program. The incidence of post-transport CPV diagnoses in the study population of 4088 puppies was 2.3%. The number of pre-transport vaccinations, length of stay at the source shelter, and time between pre-transport vaccination and transport was not associated with the expected difference in count of post-transport CPV diagnoses (p > 0.05), and was lower in those 13–17 weeks of age (IRR = 0.08, 95% CI = 0.02–0.34, p = 0.001), 18–19 weeks of age (IRR = 0.11, 95% CI = 0.02–0.80, p = 0.029), transferred in to the source shelter (IRR = 0.31, 95% CI = 0.10–0.96, p = 0.043), and transported in the summer season (IRR = 0.07, 95% CI = 0.01–0.53, p = 0.010). When basic biosecurity practices and vaccination protocols were in place, post-transport CPV cases in puppies were few, suggesting that the timing of transport should take into account factors other than the number or timing of pre-transport vaccinations.