Burnout in animal health care providers (AHCPs), namely, veterinarians and veterinary nurses, is highly prevalent. Although empathy can be a potential risk factor for burnout in these professionals, research has not empirically addressed the association between empathy and AHCP burnout. This study’s main aims were: (a) to analyze the association between empathy and burnout for AHCPs, distinguishing affective and cognitive empathy toward humans and empathy toward animals; (b) to analyze the possible protective effects of justice perceptions, professional identification, and meaningful work, to counteract the negative impact of empathy on burnout; and (c) to extend analyses to control for variables that might act as burnout protectors or risk factors, such as gender, years of professional experience, workload, income, and the perception that professionals suffer when performing euthanasia procedures. Convenience samples of 229 veterinarians and 96 veterinary nurses were collected in Portugal. The participants were invited to complete an anonymous online survey with self-reported measures. The measures used assessed burnout (exhaustion and disengagement), empathy for humans (cognitive and affective) and empathy for animals, justice perceptions, professional identification, and meaningful work. Multiple regression analysis showed that affective empathy was a significant risk factor for exhaustion in veterinarians and veterinary nurses. Empathy for animals was a significant risk factor for veterinarian exhaustion. Neither of the measures of empathy was a significant predictor of disengagement for veterinarians or veterinary nurses. Professional identification and justice perceptions, namely belief in a just world, were found to be significant burnout protectors. It is recommended that justice perceptions and professional identification should receive special attention in interventions to prevent and/or reduce burnout among AHCPs. The alternative possibility of preventing burnout through a decrease in empathy is not advisable, however, because empathy is a vital AHCP skill.