Background: Health sciences educators should increase the critical thinking of their students as this may improve the quality of care. However, this is rarely considered as a critical point in teaching, despite studies identifying factors such as the learning environment and emotional intelligence as increasing critical thinking at an undergraduate level. Thus, there is a need to better explore these factors and investigate interrelations and ways of improving critical thinking, especially in the critical field of healthcare students (nursing and medicine). Objectives: The present study aimed to examine the potential relationships between critical thinking with emotional intelligence and the learning environment. Method: This was a descriptive cross-sectional study with 208 first year health sciences university students of two nursing departments and one medicine department from three universities in Greece. The Critical Thinking Disposition Scale, Dundee Ready Education Environment Measure, and Trait Emotional Intelligence-Short Form questionnaires were used to assess critical thinking, the education environment, and emotional intelligence, respectively. Results: The results demonstrate that critical thinking was positively related to emotional intelligence (β = 0.82, p < 0.001), but not to the learning environment (β = 1.06, p = 0.30). However, a structural equation modeling analysis supported the indirect relationship between the learning environment and critical thinking through emotional intelligence (M = 1.10, CI = 0.13–2.17, p < 0.05). Conclusions: Emotional intelligence may be the underlying mechanism for achieving critical thinking if it is well applied and cultivated in a learning environment. Therefore, universities could modify their curricula and place emotional intelligence at the epicenter of teaching.