Compassion fatigue has been described in various “caring professions” across the human medical field. Recently, compassion fatigue has been identified as a concern in animal care professions, specifically veterinary medicine. Despite the perceived increased risk of compassion fatigue in veterinary personnel in animal research, no rigorous studies have been published to assess compassion fatigue in the population. The purpose of this cross-sectional study was to describe the prevalence of compassion fatigue and compassion satisfaction, using the Professional Quality of Life Scale (ProQOL), among active duty veterinary personnel in Department of Defense animal research environments. The ProQOL measures burnout and secondary traumatic stress as representative of compassion fatigue, while also measuring the inverse of compassion fatigue: compassion satisfaction. Additionally, this study set out to identify factors associated with development of compassion fatigue and satisfaction. Validated scales of measurement were used to assess the frequency of exposures and outcomes of interest, while associations were analyzed using linear regression models. The study found most survey respondents reported high levels of compassion satisfaction, and low levels of burnout and secondary traumatic stress; however, moderate levels of burnout and secondary traumatic stress were also prevalent in the population. Factors associated with higher levels of compassion fatigue (as measured by burnout and secondary traumatic stress) and decreased compassion satisfaction included working with nonhuman primates, difficulty working with primary investigators, loneliness, and euthanasia distress. These findings can inform future research efforts to explore compassion fatigue in animal research environments, as well as initiatives for program development within Department of Defense research environments to decrease occupational stress by the prevention and mitigation of compassion fatigue.