Background: Medical school is considered a critical developmental stage for students. They face many challenges and rapid changes. Unfortunately, they adopt unhealthy behaviors that can negatively affect their future health and role as healthcare providers in some cases. Objective: This research aimed to compare gender disparities in health-promoting habits among Palestinian medical students. Methods: A cross-sectional study was carried out using the HPLP II mean scores on 400 students composed of 22.25% males and 77.75% females. According to Pender's model, a self-reported anonymous questionnaire, including the health-promoting lifestyle profile II, was distributed to a convenient sample of students during the Spring of 2018. Data analysis was performed using descriptive analysis and parametric tests. Results: Gender differences in the total health-promoting lifestyle profile II scores and health responsibility were significant, with females having higher scores than males. Males were more significantly engaged in the physical activity subscale than females (p < 0.01). Females scored significantly higher than males in the interpersonal relations subscale (p < 0.001). Gender differences in other subscales were statistically insignificant. Conclusions: This study might give healthcare providers and educators insights into developing specific warranted interventions and gender-sensitive measures to orient medical students towards better healthy lifestyles. Medical schools are invited to prioritize healthy styles and behaviors based on gender in the curriculum.