Objectives The purpose of this study was to explore the domains of emotional intelligence among medical students and ascertain its relationship to academic achievement. Method: A cross-sectional study was conducted on 2340 undergraduate medical students from different Egyptian and Saudi Arabian universities using a semi-structured online abstract including two parts: Socio-demographic data and emotional intelligence questionnaire. Results The study was conducted on 2340 medical students aged (21.5 ± 1.9, range = 17–24 years) from two countries, Saudi Arabia (28.8%) and Egypt (71.2%). Females represented 68.4%. Academic achievement was distributed as excellent 54.1%, very good (28%), good (14.5%) and accepted (3.4%). The total EI score reported that 63.9% of the students had strength while 35.9% needed attention. Managing emotion, motivating oneself and total EI score were significantly higher among Egyptian students in comparison to Saudi Arabia students (P < 0.001). Females showed significantly higher EI scores than males. Egyptian males showed significantly higher EI scores than Saudi Arabian males (P < 0.001). Self-awareness was significantly high in Saudi Arabian females while managing emotions was significantly high among Egyptian females (P < 0.01). Academic achievement showed that EI scores were significantly higher among very good and excellent achievement in comparison to good or accepted achievement except self-awareness which showed that those with accepted achievement had higher self-awareness than those with high achievement. Significant positive correlation was found between EI scores and academic achievement (P < 0.001) Conclusion Emotional intelligence domains relate significantly to academic achievements in medical students. Therefore, this study recommended the necessity of improving the students ‘emotional intelligence in the scientific and community environment with proper interventions strategies through developing program that enhances their academic achievement to play a pivotal role when transforming into business world and recently in academic study.