Abstract Background Professional development of public health leaders requires a form of instruction which is competency-based to help them develop the abilities to address complex and evolving demands of health care systems. Concurrently, emotional intelligence (EI) is a key to organisational success. Our aim was twofold: i) to assess the relationship between the level of self-assessed public health and EI competencies among Master of European Public Health (MEPH) students and graduates at Maastricht University, and; ii) to determine the relationship between different groups of public health competencies and specific EI skills. Methods A cross-sectional study was conducted including all recent MEPH graduates and students from 2009–2012, out of 67 eligible candidates N = 51 were contacted and N = 33 responded (11 males and 22 females; overall response: 64.7%).Two validated tools were employed: i) public health competencies self-assessment questionnaire, and; ii) Assessing Emotions Scale. Results Females scored higher than males in all seven domains of the self-assessed key public health competencies (NS) and emotional intelligence competences (P = 0.022). Overall, the mean value of public health competencies was the lowest in students with “staff” preferences and the highest among students with mixed job preferences (P