The aim of this study was to investigate lifestyle habits in health and non-health science students from the University of Split, Croatia, and to evaluate their association with perceived stress and psychological well-being. We surveyed 783 students during February–March 2021. Hierarchical multiple regression analysis was used in the analysis. Health science students spent less time using screens, were sitting less, slept less, but also showed better compliance with the Mediterranean diet compared to non-health science students (10.6% vs. 5.9%). There were no differences in stress and well-being perception between the two study groups. Female gender, lack of sleep, less daily sitting time, anxiety, and lower optimism were associated with higher stress in non-health science students, while anxiousness and more sitting were found to be significant among health students. Well-being among health science students was positively associated with BMI, having had COVID-19, being refreshed after waking up during working days, Mediterranean diet adherence, health perception, optimism, and quality of life, and negatively with TV time and anxiousness. Shorter sleep duration on non-working days, feeling refreshed after waking up on non-working days, higher quality of life and optimism, and lower anxiousness were associated with higher well-being among non-health students. Identifying unhealthy lifestyle habits in students is essential for implementing targeted interventions to better their health outcomes.