Background: Entrance to a university is associated with a range of stressful academic, cognitive and emotional resources, and students may be frustrated and conflicted when experiencing these pressures as well as they may exhibit a range of psychological responses. Objectives: This study aimed at designing an educational program for mindfulness and its effectiveness in students' cognitive, emotional, and educational processes. Methods: The study was conducted by descriptive-correlational method among third-year medical students of Tehran University of Medical Sciences in 2017-18. The statistical population included 250 people. The sample size was determined at 30 patients by power analysis method for conducting a quasi-experimental intervention with two 1.5-month and 3-month follow-up. Data collection tools included Bauer's mindfulness questionnaire (2006), Cassidy and Long's Scale of Problem-Solving (1996), Maslach burnout inventory (2002), Dillon and Grout academic alienation scale (1976), and Grant and Langford self-reflection and insight scale (2002). Cronbach's alpha coefficients of tools in this study were 0.75 for Bauer's questionnaire, 0.70 for Cassidy and Long's scale, 0.70 for Maslach, 0.73 for Grant and Langford, and 0.71 for Dillon and Grout. The intervention program was designed based on the Roeser and Schunert-Reichl (2016) mindfulness program. The face validity of the program was assessed by Fortalza Tool (2017) and a pilot study was carried out. Results (P < 0.01) were significant, indicating the acceptance of the designed package. Descriptive statistics and homogeneity tests, analysis of variance (ANOVA) and repeated measures multivariate analysis were performed with SPSS 23 software for statistical investigation. Results: The findings showed that at P < 0.01, mindfulness training program had a significant positive effect on all components of problem-solving ability and academic alienation. Mindfulness do not affect the environmentalism of emotional mindfulness (P < 0.05) and the pessimism component of academic burnout (P < 0.05). In all of the components, the sphericity assumption of the spatial distribution and the Levin test and the normal distribution were observed. Conclusions: Mindfulness education program can affect students' cognitive and emotional processes and can be effective in reducing educational problems such as academic burnout and academic alienation, meanwhile, in increasing problem-solving and emotional mindfulness. It is recommended that this educational program should be implemented for new students of the universities.