COVID-19 caused great difficulties in many people’s daily lives, including university students in Japan. This study examined whether living with companion animals and attachment to companion animals influence the moods of university students. Students answered a questionnaire, including demographic data, companion animal ownership, attachment to their companion animals, perceived difficulties from COVID-19, and Profile of Mood States 2 (POMS2) results. A total of 180 students answered the questionnaire. Stepwise multiple regression analyses were conducted to identify factors related to the total mood disturbance (TMD) score of the POMS2. In the regression model, perceived difficulties from COVID-19 and having a companion animal and a strong attachment to their companion animals were significantly correlated with TMD and served as the predictor variables. The first variable was positively related to TMD, whereas companion animal ownership with high attachment to their companion animals was negatively related to TMD. This finding indicated that companion animal ownership with high attachment to their companion animals would relate to a positive mood in university students majoring in animal sciences during the COVID-19 pandemic. However, because of the limited population in size and by the students’ major, the results need to be interpreted as a possible effect of companion animals, and not as conclusive evidence to support the effects of animals.